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~/Projects/gene-converter $ p build_and_convert.py
docker build -t convert/elegene10st --build-arg package=pd.elegene.1.0.st_3.12.0.tar.gz --build-arg db=elegene10st -f Dockerfile.pd .
Sending build context to Docker daemon 3.904GB
Step 1/13 : FROM convert/base
---> d958adf36199
Step 2/13 : WORKDIR /home/user
Removing intermediate container a0118890d985
---> 47b27a4c2473
Step 3/13 : USER root
---> Running in 475050347cd0
Removing intermediate container 475050347cd0
---> c6cf6253bb3d
Step 4/13 : COPY install_pd.R .
---> 0e591293bbac
Step 5/13 : ARG package
---> Running in 07e2a1244c34
Removing intermediate container 07e2a1244c34
---> 2a40e6020d31
Step 6/13 : ENV PACKAGE=$package
---> Running in efb870c49c06
Removing intermediate container efb870c49c06
---> 3d7ce725ef4f
Step 7/13 : ARG db
---> Running in fb40ec396952
Removing intermediate container fb40ec396952
---> 4b4d2f2dc247
Step 8/13 : ENV DB=$db
---> Running in a2d7f0d0f1a4
Removing intermediate container a2d7f0d0f1a4
---> 2db0d7b68e07
Step 9/13 : RUN Rscript install_pd.R
---> Running in 6589c1c84c6e
Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help
A new version of Bioconductor is available after installing the most recent
version of R; see http://bioconductor.org/install
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15).
Installing package(s) 'elegene10st.db'
Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv',
'spatial'
Warning message:
package 'elegene10st.db' is not available (for R version 3.4.4)
Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.elegene.1.0.st_3.12.0.tar.gz
Installing pd.elegene.1.0.st
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
CMD INSTALL '/tmp/RtmpuPG0Nk/devtools76fe33c13/pd.elegene.1.0.st' \
--library='/usr/local/lib/R/site-library' --install-tests
* installing *source* package 'pd.elegene.1.0.st' ...
** R
** data
** inst
** preparing package for lazy loading
^[[A** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (pd.elegene.1.0.st)
[[1]]
[1] TRUE
Removing intermediate container 6589c1c84c6e
---> f80d10417c06
Step 10/13 : VOLUME /home/user/data
---> Running in 794ac02dd915
Removing intermediate container 794ac02dd915
---> 7389853cb3b5
Step 11/13 : COPY convert.R .
---> 2fb10b6f8cd3
Step 12/13 : USER user
---> Running in a05b852f4963
Removing intermediate container a05b852f4963
---> 1f8e676cfe08
Step 13/13 : ENTRYPOINT []
---> Running in c15f254f1fcb
Removing intermediate container c15f254f1fcb
---> 2f02699c9689
Successfully built 2f02699c9689
Successfully tagged convert/elegene10st:latest
docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/elegene10st Rscript convert.R -p elegene10st -o /home/user/data/out/ -i /home/user/data/elegene10st/GSM1816552_GSM1816552_AW2.CEL.gz -d elegene10st -s ce -g GSM1816552_GSM1816552_AW2
^[[ALoading required package: AnnotationDbi
Loading required package: methods
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Error in library(db_package_name, character.only = TRUE) :
there is no package called 'elegene10st.db'
Execution halted
docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/elegene10st Rscript convert.R -p elegene10st -o /home/user/data/out/ -i /home/user/data/elegene10st/GSM2648100_GSM2648100_Affy0272_13_JI2.CEL.gz -d elegene10st -s ce -g GSM2648100_GSM2648100_Affy0272_13_JI2
Loading required package: AnnotationDbi
Loading required package: methods
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Error in library(db_package_name, character.only = TRUE) :
there is no package called 'elegene10st.db'
Execution halted
docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/elegene10st Rscript convert.R -p elegene10st -o /home/user/data/out/ -i /home/user/data/elegene10st/GSM1816553_GSM1816553_AW3.CEL.gz -d elegene10st -s ce -g GSM1816553_GSM1816553_AW3
Loading required package: AnnotationDbi
Loading required package: methods
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Error in library(db_package_name, character.only = TRUE) :
there is no package called 'elegene10st.db'
Execution halted
docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/elegene10st Rscript convert.R -p elegene10st -o /home/user/data/out/ -i /home/user/data/elegene10st/GSM2816667_GSM2816667_02_Daf-21A966.CEL.gz -d elegene10st -s ce -g GSM2816667_GSM2816667_02_Daf-21A966
Loading required package: AnnotationDbi
Loading required package: methods
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Error in library(db_package_name, character.only = TRUE) :
there is no package called 'elegene10st.db'
Execution halted
docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/elegene10st Rscript convert.R -p elegene10st -o /home/user/data/out/ -i /home/user/data/elegene10st/GSM2648108_GSM2648108_Affy0272_21_6I5.CEL.gz -d elegene10st -s ce -g GSM2648108_GSM2648108_Affy0272_21_6I5
Loading required package: AnnotationDbi
Loading required package: methods
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Error in library(db_package_name, character.only = TRUE) :
there is no package called 'elegene10st.db'
Execution halted
Ran a whole brain!
docker build -t convert/cangene10st --build-arg package=pd.cangene.1.0.st_3.12.0.tar.gz --build-arg db=cangene10st -f Dockerfile.pd .
Sending build context to Docker daemon 3.904GB
Step 1/13 : FROM convert/base
---> d958adf36199
Step 2/13 : WORKDIR /home/user
---> Using cache
---> 47b27a4c2473
Step 3/13 : USER root
---> Using cache
---> c6cf6253bb3d
Step 4/13 : COPY install_pd.R .
---> Using cache
---> 0e591293bbac
Step 5/13 : ARG package
---> Using cache
---> 2a40e6020d31
Step 6/13 : ENV PACKAGE=$package
---> Running in ad29a023a437
Removing intermediate container ad29a023a437
---> 0b8d4f987ba3
Step 7/13 : ARG db
---> Running in 8094e59ffe49
Removing intermediate container 8094e59ffe49
---> a5b932ac565b
Step 8/13 : ENV DB=$db
---> Running in 88337921c360
Removing intermediate container 88337921c360
---> f43152af7d5a
Step 9/13 : RUN Rscript install_pd.R
---> Running in 61f2e6ce72f3
Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help
A new version of Bioconductor is available after installing the most recent
version of R; see http://bioconductor.org/install
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15).
Installing package(s) 'cangene10st.db'
Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv',
'spatial'
Warning message:
package 'cangene10st.db' is not available (for R version 3.4.4)
Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.cangene.1.0.st_3.12.0.tar.gz
Installing pd.cangene.1.0.st
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
CMD INSTALL '/tmp/RtmpRh6hts/devtools775013b81/pd.cangene.1.0.st' \
--library='/usr/local/lib/R/site-library' --install-tests
* installing *source* package 'pd.cangene.1.0.st' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (pd.cangene.1.0.st)
[[1]]
[1] TRUE
Removing intermediate container 61f2e6ce72f3
---> 120ed9465f4f
Step 10/13 : VOLUME /home/user/data
---> Running in ad8eab712d5e
Removing intermediate container ad8eab712d5e
---> d8be7a9249f3
Step 11/13 : COPY convert.R .
---> 2b4c8f3b28b6
Step 12/13 : USER user
---> Running in 2b81397438f9
Removing intermediate container 2b81397438f9
---> 5982ba3020d3
Step 13/13 : ENTRYPOINT []
---> Running in 72a6aed5160b
Removing intermediate container 72a6aed5160b
---> b57eb70e3f1f
Successfully built b57eb70e3f1f
Successfully tagged convert/cangene10st:latest
docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/cangene10st Rscript convert.R -p cangene10st -o /home/user/data/out/ -i /home/user/data/cangene10st/GSM1677434_GSM1677434_2656CLG0023-20131001-Canine1.0.CEL.gz -d cangene10st -s cf -g GSM1677434_GSM1677434_2656CLG0023-20131001-Canine1
Loading required package: AnnotationDbi
Loading required package: methods
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Error in library(db_package_name, character.only = TRUE) :
there is no package called 'cangene10st.db'
Execution halted
docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/cangene10st Rscript convert.R -p cangene10st -o /home/user/data/out/ -i /home/user/data/cangene10st/GSM1677428_GSM1677428_2656CLG0017-20131001-Canine1.0.CEL.gz -d cangene10st -s cf -g GSM1677428_GSM1677428_2656CLG0017-20131001-Canine1
Loading required package: AnnotationDbi
Loading required package: methods
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Error in library(db_package_name, character.only = TRUE) :
there is no package called 'cangene10st.db'
Execution halted
docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/cangene10st Rscript convert.R -p cangene10st -o /home/user/data/out/ -i /home/user/data/cangene10st/GSM1701881_GSM1701881_191.CEL.gz -d cangene10st -s cf -g GSM1701881_GSM1701881_191
Loading required package: AnnotationDbi
Loading required package: methods
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Error in library(db_package_name, character.only = TRUE) :
there is no package called 'cangene10st.db'
Execution halted
docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/cangene10st Rscript convert.R -p cangene10st -o /home/user/data/out/ -i /home/user/data/cangene10st/GSM1677418_GSM1677418_2656CLG0007-20131001-Canine1.0.CEL.gz -d cangene10st -s cf -g GSM1677418_GSM1677418_2656CLG0007-20131001-Canine1
Loading required package: AnnotationDbi
Loading required package: methods
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Error in library(db_package_name, character.only = TRUE) :
there is no package called 'cangene10st.db'
Execution halted
docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/cangene10st Rscript convert.R -p cangene10st -o /home/user/data/out/ -i /home/user/data/cangene10st/GSM1701867_GSM1701867_162.CEL.gz -d cangene10st -s cf -g GSM1701867_GSM1701867_162
Loading required package: AnnotationDbi
Loading required package: methods
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Error in library(db_package_name, character.only = TRUE) :
there is no package called 'cangene10st.db'
Execution halted
Ran a whole brain!
docker build -t convert/ovigene11st --build-arg package=pd.ovigene.1.1.st_3.12.0.tar.gz --build-arg db=ovigene11st -f Dockerfile.pd .
Sending build context to Docker daemon 3.904GB
Step 1/13 : FROM convert/base
---> d958adf36199
Step 2/13 : WORKDIR /home/user
---> Using cache
---> 47b27a4c2473
Step 3/13 : USER root
---> Using cache
---> c6cf6253bb3d
Step 4/13 : COPY install_pd.R .
---> Using cache
---> 0e591293bbac
Step 5/13 : ARG package
---> Using cache
---> 2a40e6020d31
Step 6/13 : ENV PACKAGE=$package
---> Running in 12c22770371e
Removing intermediate container 12c22770371e
---> ed8f6cef637c
Step 7/13 : ARG db
---> Running in 98925382c08a
Removing intermediate container 98925382c08a
---> b8e1cca7c13a
Step 8/13 : ENV DB=$db
---> Running in 704afcf68e59
Removing intermediate container 704afcf68e59
---> 19fe7ddc96f0
Step 9/13 : RUN Rscript install_pd.R
---> Running in 5a35a2bd4c0b
Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help
A new version of Bioconductor is available after installing the most recent
version of R; see http://bioconductor.org/install
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15).
Installing package(s) 'ovigene11st.db'
Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv',
'spatial'
Warning message:
package 'ovigene11st.db' is not available (for R version 3.4.4)
Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.ovigene.1.1.st_3.12.0.tar.gz
Installing pd.ovigene.1.1.st
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
CMD INSTALL '/tmp/Rtmp8iuxh3/devtools726822ac3/pd.ovigene.1.1.st' \
--library='/usr/local/lib/R/site-library' --install-tests
* installing *source* package 'pd.ovigene.1.1.st' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (pd.ovigene.1.1.st)
[[1]]
[1] TRUE
Removing intermediate container 5a35a2bd4c0b
---> 7a67908e7b05
Step 10/13 : VOLUME /home/user/data
---> Running in 7263ac2e3ed4
Removing intermediate container 7263ac2e3ed4
---> 37d8a9c6183a
Step 11/13 : COPY convert.R .
---> 2d4bf529b79b
Step 12/13 : USER user
---> Running in 690c59aea37e
Removing intermediate container 690c59aea37e
---> c55a83882be0
Step 13/13 : ENTRYPOINT []
---> Running in ec326444094f
Removing intermediate container ec326444094f
---> a60ca2d1206e
Successfully built a60ca2d1206e
Successfully tagged convert/ovigene11st:latest
docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/ovigene11st Rscript convert.R -p ovigene11st -o /home/user/data/out/ -i /home/user/data/ovigene11st/GSM1556961_GSM1556961_1883.CEL.gz -d ovigene11st -s oa -g GSM1556961_GSM1556961_1883
Loading required package: AnnotationDbi
Loading required package: methods
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Error in library(db_package_name, character.only = TRUE) :
there is no package called 'ovigene11st.db'
Execution halted
docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/ovigene11st Rscript convert.R -p ovigene11st -o /home/user/data/out/ -i /home/user/data/ovigene11st/GSM1556974_GSM1556974_1947.CEL.gz -d ovigene11st -s oa -g GSM1556974_GSM1556974_1947
Loading required package: AnnotationDbi
Loading required package: methods
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Error in library(db_package_name, character.only = TRUE) :
there is no package called 'ovigene11st.db'
Execution halted
Ran a whole brain!
docker build -t convert/hugene20st --build-arg package=pd.hugene.2.0.st_3.14.1.tar.gz --build-arg db=hugene20stprobeset -f Dockerfile.pd .
Sending build context to Docker daemon 3.904GB
Step 1/13 : FROM convert/base
---> d958adf36199
Step 2/13 : WORKDIR /home/user
---> Using cache
---> 47b27a4c2473
Step 3/13 : USER root
---> Using cache
---> c6cf6253bb3d
Step 4/13 : COPY install_pd.R .
---> Using cache
---> 0e591293bbac
Step 5/13 : ARG package
---> Using cache
---> 2a40e6020d31
Step 6/13 : ENV PACKAGE=$package
---> Running in de30520db63d
Removing intermediate container de30520db63d
---> 6d8c9f0bac8b
Step 7/13 : ARG db
---> Running in 6329e9c9e8ce
Removing intermediate container 6329e9c9e8ce
---> 2124b99a4817
Step 8/13 : ENV DB=$db
---> Running in 10a5733eda98
Removing intermediate container 10a5733eda98
---> 0822bbb1d589
Step 9/13 : RUN Rscript install_pd.R
---> Running in 2d3dfc7f47a9
Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help
A new version of Bioconductor is available after installing the most recent
version of R; see http://bioconductor.org/install
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15).
Installing package(s) 'hugene20stprobeset.db'
trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/hugene20stprobeset.db_8.7.0.tar.gz'
Content type 'application/x-gzip' length 30602383 bytes (29.2 MB)
==================================================
downloaded 29.2 MB
* installing *source* package 'hugene20stprobeset.db' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (hugene20stprobeset.db)
The downloaded source packages are in
'/tmp/RtmpHhkYp5/downloaded_packages'
Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv',
'spatial'
Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.hugene.2.0.st_3.14.1.tar.gz
Installing pd.hugene.2.0.st
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
CMD INSTALL '/tmp/RtmpHhkYp5/devtools6596af61/pd.hugene.2.0.st' \
--library='/usr/local/lib/R/site-library' --install-tests
* installing *source* package 'pd.hugene.2.0.st' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (pd.hugene.2.0.st)
[[1]]
[1] TRUE
Removing intermediate container 2d3dfc7f47a9
---> c54443f4a7f8
Step 10/13 : VOLUME /home/user/data
---> Running in 73faeea6c135
Removing intermediate container 73faeea6c135
---> 16a7a913e327
Step 11/13 : COPY convert.R .
---> 246071e32bca
Step 12/13 : USER user
---> Running in ade11701e946
Removing intermediate container ade11701e946
---> d3cba171257a
Step 13/13 : ENTRYPOINT []
---> Running in 3b4bff5de490
Removing intermediate container 3b4bff5de490
---> 6b928d84aa2c
Successfully built 6b928d84aa2c
Successfully tagged convert/hugene20st:latest
docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hugene20st Rscript convert.R -p hugene20st -o /home/user/data/out/ -i /home/user/data/hugene20st/GSM2080888_GSM2080888_8_treg_stim_HuGene-2_0-st_.CEL -d hugene20stprobeset -s hs -g GSM2080888_GSM2080888_8_treg_stim_HuGene-2_0-st_
Loading required package: AnnotationDbi
Loading required package: methods
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: org.Hs.eg.db
Reading..
Loading required package: pd.hugene.2.0.st
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: RSQLite
Loading required package: oligoClasses
Welcome to oligoClasses version 1.40.0
Loading required package: oligo
================================================================================
Welcome to oligo version 1.42.0
================================================================================
Loading required package: DBI
Platform design info loaded.
Reading in : /home/user/data/hugene20st/GSM2080888_GSM2080888_8_treg_stim_HuGene-2_0-st_.CEL
Mutating..
Joining..
Interesectiong..
Selecting..
docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hugene20st Rscript convert.R -p hugene20st -o /home/user/data/out/ -i /home/user/data/hugene20st/GSM2080886_GSM2080886_6_th_stim_HuGene-2_0-st_.CEL.gz -d hugene20stprobeset -s hs -g GSM2080886_GSM2080886_6_th_stim_HuGene-2_0-st_
Loading required package: AnnotationDbi
Loading required package: methods
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: org.Hs.eg.db
Reading..
Loading required package: pd.hugene.2.0.st
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: RSQLite
Loading required package: oligoClasses
Welcome to oligoClasses version 1.40.0
Loading required package: oligo
================================================================================
Welcome to oligo version 1.42.0
================================================================================
Loading required package: DBI
Platform design info loaded.
Reading in : /home/user/data/hugene20st/GSM2080886_GSM2080886_6_th_stim_HuGene-2_0-st_.CEL.gz
Mutating..
Joining..
Interesectiong..
Selecting..
docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hugene20st Rscript convert.R -p hugene20st -o /home/user/data/out/ -i /home/user/data/hugene20st/GSM2080888_GSM2080888_8_treg_stim_HuGene-2_0-st_.CEL.gz -d hugene20stprobeset -s hs -g GSM2080888_GSM2080888_8_treg_stim_HuGene-2_0-st_
Loading required package: AnnotationDbi
Loading required package: methods
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: org.Hs.eg.db
Reading..
Loading required package: pd.hugene.2.0.st
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: RSQLite
Loading required package: oligoClasses
Welcome to oligoClasses version 1.40.0
Loading required package: oligo
================================================================================
Welcome to oligo version 1.42.0
================================================================================
Loading required package: DBI
Platform design info loaded.
Reading in : /home/user/data/hugene20st/GSM2080888_GSM2080888_8_treg_stim_HuGene-2_0-st_.CEL.gz
Mutating..
Joining..
Interesectiong..
Selecting..
^[[Adocker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hugene20st Rscript convert.R -p hugene20st -o /home/user/data/out/ -i /home/user/data/hugene20st/GSM2080887_GSM2080887_7_treg_ctr_HuGene-2_0-st_.CEL.gz -d hugene20stprobeset -s hs -g GSM2080887_GSM2080887_7_treg_ctr_HuGene-2_0-st_
Loading required package: AnnotationDbi
Loading required package: methods
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: org.Hs.eg.db
Reading..
Loading required package: pd.hugene.2.0.st
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: RSQLite
Loading required package: oligoClasses
Welcome to oligoClasses version 1.40.0
Loading required package: oligo
================================================================================
Welcome to oligo version 1.42.0
================================================================================
Loading required package: DBI
Platform design info loaded.
Reading in : /home/user/data/hugene20st/GSM2080887_GSM2080887_7_treg_ctr_HuGene-2_0-st_.CEL.gz
Mutating..
Joining..
Interesectiong..
Selecting..
docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hugene20st Rscript convert.R -p hugene20st -o /home/user/data/out/ -i /home/user/data/hugene20st/GSM2080885_GSM2080885_5_th_ctr_HuGene-2_0-st_.CEL.gz -d hugene20stprobeset -s hs -g GSM2080885_GSM2080885_5_th_ctr_HuGene-2_0-st_
Loading required package: AnnotationDbi
Loading required package: methods
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: org.Hs.eg.db
Reading..
Loading required package: pd.hugene.2.0.st
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: RSQLite
Loading required package: oligoClasses
Welcome to oligoClasses version 1.40.0
Loading required package: oligo
================================================================================
Welcome to oligo version 1.42.0
================================================================================
Loading required package: DBI
Platform design info loaded.
Reading in : /home/user/data/hugene20st/GSM2080885_GSM2080885_5_th_ctr_HuGene-2_0-st_.CEL.gz
Mutating..
Joining..
Interesectiong..
Selecting..
docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hugene20st Rscript convert.R -p hugene20st -o /home/user/data/out/ -i /home/user/data/hugene20st/GSM2080883_GSM2080883_3_treg_ctr_HuGene-2_0-st_.CEL.gz -d hugene20stprobeset -s hs -g GSM2080883_GSM2080883_3_treg_ctr_HuGene-2_0-st_
Loading required package: AnnotationDbi
Loading required package: methods
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: org.Hs.eg.db
Reading..
Loading required package: pd.hugene.2.0.st
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: RSQLite
Loading required package: oligoClasses
Welcome to oligoClasses version 1.40.0
Loading required package: oligo
================================================================================
Welcome to oligo version 1.42.0
================================================================================
Loading required package: DBI
Platform design info loaded.
Reading in : /home/user/data/hugene20st/GSM2080883_GSM2080883_3_treg_ctr_HuGene-2_0-st_.CEL.gz
Mutating..
Joining..
Interesectiong..
Selecting..
Ran a whole brain!
docker build -t convert/mogene11st --build-arg package=pd.mogene.1.1.st.v1_3.14.1.tar.gz --build-arg db=mogene11stprobeset -f Dockerfile.pd .
Sending build context to Docker daemon 3.904GB
Step 1/13 : FROM convert/base
---> d958adf36199
Step 2/13 : WORKDIR /home/user
---> Using cache
---> 47b27a4c2473
Step 3/13 : USER root
---> Using cache
---> c6cf6253bb3d
Step 4/13 : COPY install_pd.R .
---> Using cache
---> 0e591293bbac
Step 5/13 : ARG package
---> Using cache
---> 2a40e6020d31
Step 6/13 : ENV PACKAGE=$package
---> Running in d19fa305a6ce
Removing intermediate container d19fa305a6ce
---> c8c788f3723a
Step 7/13 : ARG db
---> Running in cf8205ab7de3
Removing intermediate container cf8205ab7de3
---> 9187d93cc46f
Step 8/13 : ENV DB=$db
---> Running in fb57f0df7c3c
Removing intermediate container fb57f0df7c3c
---> d313f1389cee
Step 9/13 : RUN Rscript install_pd.R
---> Running in 7ee5e849e6c8
Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help
A new version of Bioconductor is available after installing the most recent
version of R; see http://bioconductor.org/install
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15).
Installing package(s) 'mogene11stprobeset.db'
trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/mogene11stprobeset.db_8.7.0.tar.gz'
Content type 'application/x-gzip' length 19287229 bytes (18.4 MB)
==================================================
downloaded 18.4 MB
* installing *source* package 'mogene11stprobeset.db' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (mogene11stprobeset.db)
The downloaded source packages are in
'/tmp/Rtmpu0ObUF/downloaded_packages'
Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv',
'spatial'
Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.mogene.1.1.st.v1_3.14.1.tar.gz
Installing pd.mogene.1.1.st.v1
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
CMD INSTALL '/tmp/Rtmpu0ObUF/devtools7572a4ea/pd.mogene.1.1.st.v1' \
--library='/usr/local/lib/R/site-library' --install-tests
* installing *source* package 'pd.mogene.1.1.st.v1' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (pd.mogene.1.1.st.v1)
[[1]]
[1] TRUE
Removing intermediate container 7ee5e849e6c8
---> 11e6e09836bd
Step 10/13 : VOLUME /home/user/data
---> Running in 47c33d94520b
Removing intermediate container 47c33d94520b
---> 25307936c617
Step 11/13 : COPY convert.R .
---> 8f6107d8c529
Step 12/13 : USER user
---> Running in 1d04864adc2e
Removing intermediate container 1d04864adc2e
---> 1cf446c0806c
Step 13/13 : ENTRYPOINT []
---> Running in bbdfdb6718ae
Removing intermediate container bbdfdb6718ae
---> c8f2c729ce4e
Successfully built c8f2c729ce4e
Successfully tagged convert/mogene11st:latest
docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/mogene11st Rscript convert.R -p mogene11st -o /home/user/data/out/ -i /home/user/data/mogene11st/GSM1495810_GSM1495810_HTMoGene11_022312W_PB115_S374_7_RNA.CEL.gz -d mogene11stprobeset -s mm -g GSM1495810_GSM1495810_HTMoGene11_022312W_PB115_S374_7_RNA
Error: CEL file header does not match platform argument
Execution halted
docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/mogene11st Rscript convert.R -p mogene11st -o /home/user/data/out/ -i /home/user/data/mogene11st/GSM1495834_GSM1495834_HTMoGene11_022312W_PB99_S386_13LiverB.CEL.gz -d mogene11stprobeset -s mm -g GSM1495834_GSM1495834_HTMoGene11_022312W_PB99_S386_13LiverB
Error: CEL file header does not match platform argument
Execution halted
docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/mogene11st Rscript convert.R -p mogene11st -o /home/user/data/out/ -i /home/user/data/mogene11st/GSM1495805_GSM1495805_HTMoGene11_022312W_PB110_S374_2_RNA.CEL.gz -d mogene11stprobeset -s mm -g GSM1495805_GSM1495805_HTMoGene11_022312W_PB110_S374_2_RNA
Error: CEL file header does not match platform argument
Execution halted
docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/mogene11st Rscript convert.R -p mogene11st -o /home/user/data/out/ -i /home/user/data/mogene11st/GSM1495809_GSM1495809_HTMoGene11_022312W_PB114_S374_6_RNA.CEL.gz -d mogene11stprobeset -s mm -g GSM1495809_GSM1495809_HTMoGene11_022312W_PB114_S374_6_RNA
Error: CEL file header does not match platform argument
Execution halted
docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/mogene11st Rscript convert.R -p mogene11st -o /home/user/data/out/ -i /home/user/data/mogene11st/GSM1495822_GSM1495822_HTMoGene11_022912W_PB127_S374_19_RNA.CEL.gz -d mogene11stprobeset -s mm -g GSM1495822_GSM1495822_HTMoGene11_022912W_PB127_S374_19_RNA
Error: CEL file header does not match platform argument
Execution halted
Ran a whole brain!
docker build -t convert/bovgene11st --build-arg package=pd.bovgene.1.1.st_3.12.0.tar.gz --build-arg db=bovgene11st -f Dockerfile.pd .
Sending build context to Docker daemon 3.904GB
Step 1/13 : FROM convert/base
---> d958adf36199
Step 2/13 : WORKDIR /home/user
---> Using cache
---> 47b27a4c2473
Step 3/13 : USER root
---> Using cache
---> c6cf6253bb3d
Step 4/13 : COPY install_pd.R .
---> Using cache
---> 0e591293bbac
Step 5/13 : ARG package
---> Using cache
---> 2a40e6020d31
Step 6/13 : ENV PACKAGE=$package
---> Running in ad367bf351da
Removing intermediate container ad367bf351da
---> f28e2e8150a1
Step 7/13 : ARG db
---> Running in a643869d5aee
Removing intermediate container a643869d5aee
---> 477c99a159ab
Step 8/13 : ENV DB=$db
---> Running in f034dfbce986
Removing intermediate container f034dfbce986
---> b6ab68b02d75
Step 9/13 : RUN Rscript install_pd.R
---> Running in 196d0239233a
Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help
A new version of Bioconductor is available after installing the most recent
version of R; see http://bioconductor.org/install
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15).
Installing package(s) 'bovgene11st.db'
Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv',
'spatial'
Warning message:
package 'bovgene11st.db' is not available (for R version 3.4.4)
Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.bovgene.1.1.st_3.12.0.tar.gz
Installing pd.bovgene.1.1.st
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
CMD INSTALL '/tmp/RtmpA4t6tr/devtools722089cea/pd.bovgene.1.1.st' \
--library='/usr/local/lib/R/site-library' --install-tests
* installing *source* package 'pd.bovgene.1.1.st' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (pd.bovgene.1.1.st)
[[1]]
[1] TRUE
Removing intermediate container 196d0239233a
---> af0d1286094c
Step 10/13 : VOLUME /home/user/data
---> Running in a2ace11db845
Removing intermediate container a2ace11db845
---> d63d6f236e31
Step 11/13 : COPY convert.R .
---> fb75ef8fe4db
Step 12/13 : USER user
---> Running in 3ef7fb2ec319
Removing intermediate container 3ef7fb2ec319
---> 31a202560151
Step 13/13 : ENTRYPOINT []
---> Running in b710207d47e2
Removing intermediate container b710207d47e2
---> 7d8dc8346778
Successfully built 7d8dc8346778
Successfully tagged convert/bovgene11st:latest
docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/bovgene11st Rscript convert.R -p bovgene11st -o /home/user/data/out/ -i /home/user/data/bovgene11st/GSM1843302_GSM1843302_2031M0024_NCP+LPS.CEL.gz -d bovgene11st -s bt -g GSM1843302_GSM1843302_2031M0024_NCP+LPS
Loading required package: AnnotationDbi
Loading required package: methods
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Error in library(db_package_name, character.only = TRUE) :
there is no package called 'bovgene11st.db'
Execution halted
docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/bovgene11st Rscript convert.R -p bovgene11st -o /home/user/data/out/ -i /home/user/data/bovgene11st/GSM1843300_GSM1843300_2031M0022_CONT+LPS.CEL.gz -d bovgene11st -s bt -g GSM1843300_GSM1843300_2031M0022_CONT+LPS
Loading required package: AnnotationDbi
Loading required package: methods
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Error in library(db_package_name, character.only = TRUE) :
there is no package called 'bovgene11st.db'
Execution halted
Ran a whole brain!
docker build -t convert/clariomshumanht --build-arg package=pd.clariom.s.human.ht_3.14.1.tar.gz --build-arg db=clariomshumanht -f Dockerfile.pd .
Sending build context to Docker daemon 2.627GB
Sending build context to Docker daemon 3.904GB
Step 1/13 : FROM convert/base
---> d958adf36199
Step 2/13 : WORKDIR /home/user
---> Using cache
---> 47b27a4c2473
Step 3/13 : USER root
---> Using cache
---> c6cf6253bb3d
Step 4/13 : COPY install_pd.R .
---> Using cache
---> 0e591293bbac
Step 5/13 : ARG package
---> Using cache
---> 2a40e6020d31
Step 6/13 : ENV PACKAGE=$package
---> Running in dded58c4545d
Removing intermediate container dded58c4545d
---> 49178a8f8169
Step 7/13 : ARG db
---> Running in a897f65fadae
Removing intermediate container a897f65fadae
---> f2441683d3a8
Step 8/13 : ENV DB=$db
---> Running in a0041ebe74e4
Removing intermediate container a0041ebe74e4
---> b9202be60dec
Step 9/13 : RUN Rscript install_pd.R
---> Running in 938584e0021d
Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help
A new version of Bioconductor is available after installing the most recent
version of R; see http://bioconductor.org/install
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15).
Installing package(s) 'clariomshumanht.db'
Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv',
'spatial'
Warning message:
package 'clariomshumanht.db' is not available (for R version 3.4.4)
Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.clariom.s.human.ht_3.14.1.tar.gz
Installing pd.clariom.s.human.ht
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
CMD INSTALL '/tmp/RtmpjHUH1F/devtools74f377e2c/pd.clariom.s.human.ht' \
--library='/usr/local/lib/R/site-library' --install-tests
* installing *source* package 'pd.clariom.s.human.ht' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (pd.clariom.s.human.ht)
[[1]]
[1] TRUE
Removing intermediate container 938584e0021d
---> 500e9fb98c15
Step 10/13 : VOLUME /home/user/data
---> Running in c323e9612fbe
Removing intermediate container c323e9612fbe
---> 51ef25010dac
Step 11/13 : COPY convert.R .
---> 9d828343e351
Step 12/13 : USER user
---> Running in f982f18fc57b
Removing intermediate container f982f18fc57b
---> a865c2edde01
Step 13/13 : ENTRYPOINT []
---> Running in 958bdf989942
Removing intermediate container 958bdf989942
---> 397a5e176257
Successfully built 397a5e176257
Successfully tagged convert/clariomshumanht:latest
[Errno 2] No such file or directory: '/Users/rjones/Projects/gene-converter/cels/clariomshumanht'
Ran a sample!
Ran a whole brain!
docker build -t convert/mgu74bv2 --build-arg package=pd.mg.u74bv2_3.12.0.tar.gz --build-arg db=mgu74bv2 -f Dockerfile.pd .
Sending build context to Docker daemon 3.904GB
Step 1/13 : FROM convert/base
---> d958adf36199
Step 2/13 : WORKDIR /home/user
---> Using cache
---> 47b27a4c2473
Step 3/13 : USER root
---> Using cache
---> c6cf6253bb3d
Step 4/13 : COPY install_pd.R .
---> Using cache
---> 0e591293bbac
Step 5/13 : ARG package
---> Using cache
---> 2a40e6020d31
Step 6/13 : ENV PACKAGE=$package
---> Running in b960c3d15d1f
Removing intermediate container b960c3d15d1f
---> d9cfbc8e05a6
Step 7/13 : ARG db
---> Running in 067ddeb966c0
Removing intermediate container 067ddeb966c0
---> 9e720b5a749e
Step 8/13 : ENV DB=$db
---> Running in 935bf8d606a7
Removing intermediate container 935bf8d606a7
---> 25a4878e94a7
Step 9/13 : RUN Rscript install_pd.R
---> Running in aa5772098c07
Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help
A new version of Bioconductor is available after installing the most recent
version of R; see http://bioconductor.org/install
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15).
Installing package(s) 'mgu74bv2.db'
trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/mgu74bv2.db_3.2.3.tar.gz'
Content type 'application/x-gzip' length 459531 bytes (448 KB)
==================================================
downloaded 448 KB
* installing *source* package 'mgu74bv2.db' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (mgu74bv2.db)
The downloaded source packages are in
'/tmp/Rtmpxr1nF4/downloaded_packages'
Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv',
'spatial'
Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.mg.u74bv2_3.12.0.tar.gz
Installing pd.mg.u74bv2
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
CMD INSTALL '/tmp/Rtmpxr1nF4/devtools712d74ac8/pd.mg.u74bv2' \
--library='/usr/local/lib/R/site-library' --install-tests
* installing *source* package 'pd.mg.u74bv2' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (pd.mg.u74bv2)
[[1]]
[1] TRUE
Removing intermediate container aa5772098c07
---> 7a0ef883c2ba
Step 10/13 : VOLUME /home/user/data
---> Running in dd8dad0c67c6
Removing intermediate container dd8dad0c67c6
---> 20b69864b47f
Step 11/13 : COPY convert.R .
---> 258970f33e6d
Step 12/13 : USER user
---> Running in b1c856d505aa
Removing intermediate container b1c856d505aa
---> 6c95f0e87b77
Step 13/13 : ENTRYPOINT []
---> Running in 659c1c9e85a5
Removing intermediate container 659c1c9e85a5
---> d9bd88af1fc5
Successfully built d9bd88af1fc5
Successfully tagged convert/mgu74bv2:latest
[Errno 2] No such file or directory: '/Users/rjones/Projects/gene-converter/cels/mgu74bv2'
Ran a sample!
Ran a whole brain!
docker build -t convert/htmg430a --build-arg package=pd.ht.mg.430a_3.12.0.tar.gz --build-arg db=htmg430a -f Dockerfile.pd .
Sending build context to Docker daemon 3.904GB
Step 1/13 : FROM convert/base
---> d958adf36199
Step 2/13 : WORKDIR /home/user
---> Using cache
---> 47b27a4c2473
Step 3/13 : USER root
---> Using cache
---> c6cf6253bb3d
Step 4/13 : COPY install_pd.R .
---> Using cache
---> 0e591293bbac
Step 5/13 : ARG package
---> Using cache
---> 2a40e6020d31
Step 6/13 : ENV PACKAGE=$package
---> Running in acd0c9250cdf
Removing intermediate container acd0c9250cdf
---> 48d53611bcad
Step 7/13 : ARG db
---> Running in 75876237787a
Removing intermediate container 75876237787a
---> da7b9fb6883a
Step 8/13 : ENV DB=$db
---> Running in 796a30904531
Removing intermediate container 796a30904531
---> 0a7f36781551
Step 9/13 : RUN Rscript install_pd.R
---> Running in 3b3ce2b2f843
Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help
A new version of Bioconductor is available after installing the most recent
version of R; see http://bioconductor.org/install
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15).
Installing package(s) 'htmg430a.db'
Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv',
'spatial'
Warning message:
package 'htmg430a.db' is not available (for R version 3.4.4)
Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.ht.mg.430a_3.12.0.tar.gz
Installing pd.ht.mg.430a
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
CMD INSTALL '/tmp/RtmptUjD9Z/devtools767eb97b9/pd.ht.mg.430a' \
--library='/usr/local/lib/R/site-library' --install-tests
* installing *source* package 'pd.ht.mg.430a' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (pd.ht.mg.430a)
[[1]]
[1] TRUE
Removing intermediate container 3b3ce2b2f843
---> c6a206589d4e
Step 10/13 : VOLUME /home/user/data
---> Running in 535e54c408d3
Removing intermediate container 535e54c408d3
---> 635227162fd1
Step 11/13 : COPY convert.R .
---> 5c21f668bd22
Step 12/13 : USER user
---> Running in cf71b1341711
Removing intermediate container cf71b1341711
---> 78ad2e00f3ca
Step 13/13 : ENTRYPOINT []
---> Running in 225b566a2b75
Removing intermediate container 225b566a2b75
---> 19e966cd0163
Successfully built 19e966cd0163
Successfully tagged convert/htmg430a:latest
[Errno 2] No such file or directory: '/Users/rjones/Projects/gene-converter/cels/htmg430a'
Ran a sample!
Ran a whole brain!
docker build -t convert/bovgene10st --build-arg package=pd.bovgene.1.0.st_3.12.0.tar.gz --build-arg db=bovgene10st -f Dockerfile.pd .
Sending build context to Docker daemon 3.904GB
Step 1/13 : FROM convert/base
---> d958adf36199
Step 2/13 : WORKDIR /home/user
---> Using cache
---> 47b27a4c2473
Step 3/13 : USER root
---> Using cache
---> c6cf6253bb3d
Step 4/13 : COPY install_pd.R .
---> Using cache
---> 0e591293bbac
Step 5/13 : ARG package
---> Using cache
---> 2a40e6020d31
Step 6/13 : ENV PACKAGE=$package
---> Running in 12b6e27f3fce
Removing intermediate container 12b6e27f3fce
---> 9437b99a3dc8
Step 7/13 : ARG db
---> Running in 49099e3b7129
Removing intermediate container 49099e3b7129
---> 0c2e90c3829c
Step 8/13 : ENV DB=$db
---> Running in f9158d2a08e6
Removing intermediate container f9158d2a08e6
---> 87ae7a1662fb
Step 9/13 : RUN Rscript install_pd.R
---> Running in 683513f073d5
Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help
A new version of Bioconductor is available after installing the most recent
version of R; see http://bioconductor.org/install
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15).
Installing package(s) 'bovgene10st.db'
Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv',
'spatial'
Warning message:
package 'bovgene10st.db' is not available (for R version 3.4.4)
Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.bovgene.1.0.st_3.12.0.tar.gz
Installing pd.bovgene.1.0.st
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
CMD INSTALL '/tmp/RtmpCpTMQB/devtools747def76a/pd.bovgene.1.0.st' \
--library='/usr/local/lib/R/site-library' --install-tests
* installing *source* package 'pd.bovgene.1.0.st' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (pd.bovgene.1.0.st)
[[1]]
[1] TRUE
Removing intermediate container 683513f073d5
---> e9be9d554b4c
Step 10/13 : VOLUME /home/user/data
---> Running in 76eceb097098
Removing intermediate container 76eceb097098
---> 9cf61f5af347
Step 11/13 : COPY convert.R .
---> b1bfbc1df3de
Step 12/13 : USER user
---> Running in e6e06acaa1e3
Removing intermediate container e6e06acaa1e3
---> 09c0dce2caa8
Step 13/13 : ENTRYPOINT []
---> Running in 8eeede1ce702
Removing intermediate container 8eeede1ce702
---> 19ae02c1aead
Successfully built 19ae02c1aead
Successfully tagged convert/bovgene10st:latest
docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/bovgene10st Rscript convert.R -p bovgene10st -o /home/user/data/out/ -i /home/user/data/bovgene10st/GSM2844206_GSM2844206_V_66042_s30_LLC4.CEL.gz -d bovgene10st -s bt -g GSM2844206_GSM2844206_V_66042_s30_LLC4
Loading required package: AnnotationDbi
Loading required package: methods
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Error in library(db_package_name, character.only = TRUE) :
there is no package called 'bovgene10st.db'
Execution halted
docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/bovgene10st Rscript convert.R -p bovgene10st -o /home/user/data/out/ -i /home/user/data/bovgene10st/GSM1954042_GSM1954042_Segfam_NNR_WT_2.CEL.gz -d bovgene10st -s bt -g GSM1954042_GSM1954042_Segfam_NNR_WT_2
Error: CEL file header does not match platform argument
Execution halted
docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/bovgene10st Rscript convert.R -p bovgene10st -o /home/user/data/out/ -i /home/user/data/bovgene10st/GSM1954065_GSM1954065_Segfam_NNR_WT_25.CEL.gz -d bovgene10st -s bt -g GSM1954065_GSM1954065_Segfam_NNR_WT_25
Error: CEL file header does not match platform argument
Execution halted
docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/bovgene10st Rscript convert.R -p bovgene10st -o /home/user/data/out/ -i /home/user/data/bovgene10st/GSM2882755_GSM2882755_4161_050416_BovGene-1_0-st_.CEL.gz -d bovgene10st -s bt -g GSM2882755_GSM2882755_4161_050416_BovGene-1_0-st_
Loading required package: AnnotationDbi
Loading required package: methods
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Error in library(db_package_name, character.only = TRUE) :
there is no package called 'bovgene10st.db'
Execution halted
docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/bovgene10st Rscript convert.R -p bovgene10st -o /home/user/data/out/ -i /home/user/data/bovgene10st/GSM2561719_GSM2561719_5_BoMac_CIT24_T1.CEL.gz -d bovgene10st -s bt -g GSM2561719_GSM2561719_5_BoMac_CIT24_T1
Loading required package: AnnotationDbi
Loading required package: methods
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Error in library(db_package_name, character.only = TRUE) :
there is no package called 'bovgene10st.db'
Execution halted
Ran a whole brain!
docker build -t convert/equgene10st --build-arg package=pd.equgene.1.0.st_3.12.0.tar.gz --build-arg db=equgene10st -f Dockerfile.pd .
Sending build context to Docker daemon 3.904GB
Step 1/13 : FROM convert/base
---> d958adf36199
Step 2/13 : WORKDIR /home/user
---> Using cache
---> 47b27a4c2473
Step 3/13 : USER root
---> Using cache
---> c6cf6253bb3d
Step 4/13 : COPY install_pd.R .
---> Using cache
---> 0e591293bbac
Step 5/13 : ARG package
---> Using cache
---> 2a40e6020d31
Step 6/13 : ENV PACKAGE=$package
---> Running in 694569b0d631
Removing intermediate container 694569b0d631
---> 209eacbaffe5
Step 7/13 : ARG db
---> Running in aa730a0aa615
Removing intermediate container aa730a0aa615
---> b8c6183c8f7d
Step 8/13 : ENV DB=$db
---> Running in b893b9b26fa1
Removing intermediate container b893b9b26fa1
---> d3942c56ae6a
Step 9/13 : RUN Rscript install_pd.R
---> Running in fc8c6feddba5
Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help
A new version of Bioconductor is available after installing the most recent
version of R; see http://bioconductor.org/install
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15).
Installing package(s) 'equgene10st.db'
Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv',
'spatial'
Warning message:
package 'equgene10st.db' is not available (for R version 3.4.4)
Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.equgene.1.0.st_3.12.0.tar.gz
Installing pd.equgene.1.0.st
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
CMD INSTALL '/tmp/Rtmpo9i6jQ/devtools72fbe50f4/pd.equgene.1.0.st' \
--library='/usr/local/lib/R/site-library' --install-tests
* installing *source* package 'pd.equgene.1.0.st' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (pd.equgene.1.0.st)
[[1]]
[1] TRUE
Removing intermediate container fc8c6feddba5
---> 82c2b7d942eb
Step 10/13 : VOLUME /home/user/data
---> Running in a33680260a7d
Removing intermediate container a33680260a7d
---> 3ff79e2285a2
Step 11/13 : COPY convert.R .
---> bde9c4102805
Step 12/13 : USER user
---> Running in ed7f41f51a7f
Removing intermediate container ed7f41f51a7f
---> 58ef9b7e17eb
Step 13/13 : ENTRYPOINT []
---> Running in 029505ddceb5
Removing intermediate container 029505ddceb5
---> 33a8146d642b
Successfully built 33a8146d642b
Successfully tagged convert/equgene10st:latest
docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/equgene10st Rscript convert.R -p equgene10st -o /home/user/data/out/ -i /home/user/data/equgene10st/GSM2671023_GSM2671023_PA261_Ex_3_Dag_15_IL-1b_151015_EquGene-1_0-st.CEL.gz -d equgene10st -s ec -g GSM2671023_GSM2671023_PA261_Ex_3_Dag_15_IL-1b_151015_EquGene-1_0-st
Error in library(ba_package_name, character.only = TRUE) :
there is no package called 'equgene10stecensgprobe'
Execution halted
docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/equgene10st Rscript convert.R -p equgene10st -o /home/user/data/out/ -i /home/user/data/equgene10st/GSM2671033_GSM2671033_PA261_Ex_4_Dag_9_K_151015_EquGene-1_0-st.CEL.gz -d equgene10st -s ec -g GSM2671033_GSM2671033_PA261_Ex_4_Dag_9_K_151015_EquGene-1_0-st
Error in library(ba_package_name, character.only = TRUE) :
there is no package called 'equgene10stecensgprobe'
Execution halted
docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/equgene10st Rscript convert.R -p equgene10st -o /home/user/data/out/ -i /home/user/data/equgene10st/GSM2098343_GSM2098343_My_Crafty_Life_Week4_ESC_EquGene.CEL.gz -d equgene10st -s ec -g GSM2098343_GSM2098343_My_Crafty_Life_Week4_ESC_EquGene
Error in library(ba_package_name, character.only = TRUE) :
there is no package called 'equgene10stecensgprobe'
Execution halted
docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/equgene10st Rscript convert.R -p equgene10st -o /home/user/data/out/ -i /home/user/data/equgene10st/GSM2671012_GSM2671012_PA261_Ex_2_Dag_15_IL-1b_151007_EquGene-1_0-st.CEL.gz -d equgene10st -s ec -g GSM2671012_GSM2671012_PA261_Ex_2_Dag_15_IL-1b_151007_EquGene-1_0-st
Error in library(ba_package_name, character.only = TRUE) :
there is no package called 'equgene10stecensgprobe'
Execution halted
docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/equgene10st Rscript convert.R -p equgene10st -o /home/user/data/out/ -i /home/user/data/equgene10st/GSM1299430_GSM1299430_MG-Am3.CEL.gz -d equgene10st -s ec -g GSM1299430_GSM1299430_MG-Am3
Error in library(ba_package_name, character.only = TRUE) :
there is no package called 'equgene10stecensgprobe'
Execution halted
Ran a whole brain!
docker build -t convert/chicken --build-arg package=pd.chicken_3.12.0.tar.gz --build-arg db=chicken -f Dockerfile.pd .
Sending build context to Docker daemon 3.904GB
Step 1/13 : FROM convert/base
---> d958adf36199
Step 2/13 : WORKDIR /home/user
---> Using cache
---> 47b27a4c2473
Step 3/13 : USER root
---> Using cache
---> c6cf6253bb3d
Step 4/13 : COPY install_pd.R .
---> Using cache
---> 0e591293bbac
Step 5/13 : ARG package
---> Using cache
---> 2a40e6020d31
Step 6/13 : ENV PACKAGE=$package
---> Running in 21bfd7505bba
Removing intermediate container 21bfd7505bba
---> 851869501e47
Step 7/13 : ARG db
---> Running in c2ea7e76d1ea
Removing intermediate container c2ea7e76d1ea
---> 1094a7e62617
Step 8/13 : ENV DB=$db
---> Running in 51c6e0b3852e
Removing intermediate container 51c6e0b3852e
---> de9486bce352
Step 9/13 : RUN Rscript install_pd.R
---> Running in 4504c25e2d48
Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help
A new version of Bioconductor is available after installing the most recent
version of R; see http://bioconductor.org/install
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15).
Installing package(s) 'chicken.db'
trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/chicken.db_3.2.3.tar.gz'
Content type 'application/x-gzip' length 1520746 bytes (1.5 MB)
==================================================
downloaded 1.5 MB
* installing *source* package 'chicken.db' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (chicken.db)
The downloaded source packages are in
'/tmp/RtmpLh4ljG/downloaded_packages'
Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv',
'spatial'
Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.chicken_3.12.0.tar.gz
Installing pd.chicken
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
CMD INSTALL '/tmp/RtmpLh4ljG/devtools76d54f044/pd.chicken' \
--library='/usr/local/lib/R/site-library' --install-tests
* installing *source* package 'pd.chicken' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (pd.chicken)
[[1]]
[1] TRUE
Removing intermediate container 4504c25e2d48
---> 4066fba31783
Step 10/13 : VOLUME /home/user/data
---> Running in f6674f1996cf
Removing intermediate container f6674f1996cf
---> 688881c46d02
Step 11/13 : COPY convert.R .
---> 58f59f6e5cd4
Step 12/13 : USER user
---> Running in d0dfa9fc9a55
Removing intermediate container d0dfa9fc9a55
---> b01f1874286e
Step 13/13 : ENTRYPOINT []
---> Running in e58f119d4349
Removing intermediate container e58f119d4349
---> 8b0529028855
Successfully built 8b0529028855
Successfully tagged convert/chicken:latest
[Errno 2] No such file or directory: '/Users/rjones/Projects/gene-converter/cels/chicken'
Ran a sample!
Ran a whole brain!
docker build -t convert/rae230a --build-arg package=pd.rae230a_3.12.0.tar.gz --build-arg db=rae230a -f Dockerfile.pd .
Sending build context to Docker daemon 3.904GB
Step 1/13 : FROM convert/base
---> d958adf36199
Step 2/13 : WORKDIR /home/user
---> Using cache
---> 47b27a4c2473
Step 3/13 : USER root
---> Using cache
---> c6cf6253bb3d
Step 4/13 : COPY install_pd.R .
---> Using cache
---> 0e591293bbac
Step 5/13 : ARG package
---> Using cache
---> 2a40e6020d31
Step 6/13 : ENV PACKAGE=$package
---> Running in b4f4727df4ff
Removing intermediate container b4f4727df4ff
---> d3f14d0f71f8
Step 7/13 : ARG db
---> Running in dd5c0b238f87
Removing intermediate container dd5c0b238f87
---> 84c955c714db
Step 8/13 : ENV DB=$db
---> Running in 53b0b095baa3
Removing intermediate container 53b0b095baa3
---> ebbf30113613
Step 9/13 : RUN Rscript install_pd.R
---> Running in 54d515390f88
Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help
A new version of Bioconductor is available after installing the most recent
version of R; see http://bioconductor.org/install
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15).
Installing package(s) 'rae230a.db'
trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/rae230a.db_3.2.3.tar.gz'
Content type 'application/x-gzip' length 564338 bytes (551 KB)
==================================================
downloaded 551 KB
* installing *source* package 'rae230a.db' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (rae230a.db)
The downloaded source packages are in
'/tmp/RtmpPOMnmq/downloaded_packages'
Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv',
'spatial'
Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.rae230a_3.12.0.tar.gz
Installing pd.rae230a
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
CMD INSTALL '/tmp/RtmpPOMnmq/devtools76b0bc727/pd.rae230a' \
--library='/usr/local/lib/R/site-library' --install-tests
* installing *source* package 'pd.rae230a' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (pd.rae230a)
[[1]]
[1] TRUE
Removing intermediate container 54d515390f88
---> 70393c997183
Step 10/13 : VOLUME /home/user/data
---> Running in 339b26dd8a91
Removing intermediate container 339b26dd8a91
---> 23de53eb16cc
Step 11/13 : COPY convert.R .
---> b4645aa451ad
Step 12/13 : USER user
---> Running in 28a4bbddce78
Removing intermediate container 28a4bbddce78
---> 68c687dfeb13
Step 13/13 : ENTRYPOINT []
---> Running in fedf65bdf2d8
Removing intermediate container fedf65bdf2d8
---> 8a3a4efb80bc
Successfully built 8a3a4efb80bc
Successfully tagged convert/rae230a:latest
[Errno 2] No such file or directory: '/Users/rjones/Projects/gene-converter/cels/rae230a'
Ran a sample!
Ran a whole brain!
docker build -t convert/hugene21st --build-arg package=pd.hugene.2.1.st_3.14.1.tar.gz --build-arg db=hugene21stprobeset -f Dockerfile.pd .
Sending build context to Docker daemon 3.904GB
Step 1/13 : FROM convert/base
---> d958adf36199
Step 2/13 : WORKDIR /home/user
---> Using cache
---> 47b27a4c2473
Step 3/13 : USER root
---> Using cache
---> c6cf6253bb3d
Step 4/13 : COPY install_pd.R .
---> Using cache
---> 0e591293bbac
Step 5/13 : ARG package
---> Using cache
---> 2a40e6020d31
Step 6/13 : ENV PACKAGE=$package
---> Running in 90d50000829d
Removing intermediate container 90d50000829d
---> ff6090be2e3e
Step 7/13 : ARG db
---> Running in e3d2f96514c2
Removing intermediate container e3d2f96514c2
---> 6b911648204a
Step 8/13 : ENV DB=$db
---> Running in 00719090e862
Removing intermediate container 00719090e862
---> 60a8cec9ab42
Step 9/13 : RUN Rscript install_pd.R
---> Running in ed942fb5281e
Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help
A new version of Bioconductor is available after installing the most recent
version of R; see http://bioconductor.org/install
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15).
Installing package(s) 'hugene21stprobeset.db'
trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/hugene21stprobeset.db_8.7.0.tar.gz'
Content type 'application/x-gzip' length 30602388 bytes (29.2 MB)
==================================================
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* installing *source* package 'hugene21stprobeset.db' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (hugene21stprobeset.db)
The downloaded source packages are in
'/tmp/RtmphQJcWi/downloaded_packages'
Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv',
'spatial'
Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.hugene.2.1.st_3.14.1.tar.gz
Installing pd.hugene.2.1.st
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
CMD INSTALL '/tmp/RtmphQJcWi/devtools71c7305e3/pd.hugene.2.1.st' \
--library='/usr/local/lib/R/site-library' --install-tests
* installing *source* package 'pd.hugene.2.1.st' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (pd.hugene.2.1.st)
[[1]]
[1] TRUE
Removing intermediate container ed942fb5281e
---> 242cbc3afce1
Step 10/13 : VOLUME /home/user/data
---> Running in 57f821778551
Removing intermediate container 57f821778551
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Step 11/13 : COPY convert.R .
---> 9ff55c8b1681
Step 12/13 : USER user
---> Running in 0acd66a22dbf
Removing intermediate container 0acd66a22dbf
---> cd8b23886444
Step 13/13 : ENTRYPOINT []
---> Running in 7923bfd2af63
Removing intermediate container 7923bfd2af63
---> ff734400a975
Successfully built ff734400a975
Successfully tagged convert/hugene21st:latest
docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hugene21st Rscript convert.R -p hugene21st -o /home/user/data/out/ -i /home/user/data/hugene21st/GSM1437827_GSM1437827_HTHuGene21_102912H_SL253_810462-1.CEL.gz -d hugene21stprobeset -s hs -g GSM1437827_GSM1437827_HTHuGene21_102912H_SL253_810462-1
Loading required package: AnnotationDbi
Loading required package: methods
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: org.Hs.eg.db
Reading..
Loading required package: pd.hugene.2.1.st
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: RSQLite
Loading required package: oligoClasses
Welcome to oligoClasses version 1.40.0
Loading required package: oligo
================================================================================
Welcome to oligo version 1.42.0
================================================================================
Loading required package: DBI
Platform design info loaded.
Reading in : /home/user/data/hugene21st/GSM1437827_GSM1437827_HTHuGene21_102912H_SL253_810462-1.CEL.gz
Mutating..
Joining..
Interesectiong..
Selecting..
docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hugene21st Rscript convert.R -p hugene21st -o /home/user/data/out/ -i /home/user/data/hugene21st/GSM1437964_GSM1437964_HTHuGene21_082912H_SL22_815163-2.CEL.gz -d hugene21stprobeset -s hs -g GSM1437964_GSM1437964_HTHuGene21_082912H_SL22_815163-2
Loading required package: AnnotationDbi
Loading required package: methods
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: org.Hs.eg.db
Reading..
Loading required package: pd.hugene.2.1.st
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: RSQLite
Loading required package: oligoClasses
Welcome to oligoClasses version 1.40.0
Loading required package: oligo
================================================================================
Welcome to oligo version 1.42.0
================================================================================
Loading required package: DBI
Platform design info loaded.
Reading in : /home/user/data/hugene21st/GSM1437964_GSM1437964_HTHuGene21_082912H_SL22_815163-2.CEL.gz
Mutating..
Joining..
Interesectiong..
Selecting..
docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hugene21st Rscript convert.R -p hugene21st -o /home/user/data/out/ -i /home/user/data/hugene21st/GSM1437826_GSM1437826_HTHuGene21_100212H_SL103_810460-2.CEL.gz -d hugene21stprobeset -s hs -g GSM1437826_GSM1437826_HTHuGene21_100212H_SL103_810460-2
Loading required package: AnnotationDbi
Loading required package: methods
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: org.Hs.eg.db
Reading..
Loading required package: pd.hugene.2.1.st
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: RSQLite
Loading required package: oligoClasses
Welcome to oligoClasses version 1.40.0
Loading required package: oligo
================================================================================
Welcome to oligo version 1.42.0
================================================================================
Loading required package: DBI
Platform design info loaded.
Reading in : /home/user/data/hugene21st/GSM1437826_GSM1437826_HTHuGene21_100212H_SL103_810460-2.CEL.gz
Mutating..
Joining..
Interesectiong..
Selecting..
docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hugene21st Rscript convert.R -p hugene21st -o /home/user/data/out/ -i /home/user/data/hugene21st/GSM1437906_GSM1437906_HTHuGene21_110512H_SL284_812407-2.CEL.gz -d hugene21stprobeset -s hs -g GSM1437906_GSM1437906_HTHuGene21_110512H_SL284_812407-2
Loading required package: AnnotationDbi
Loading required package: methods
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: org.Hs.eg.db
Reading..
Loading required package: pd.hugene.2.1.st
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: RSQLite
Loading required package: oligoClasses
Welcome to oligoClasses version 1.40.0
Loading required package: oligo
================================================================================
Welcome to oligo version 1.42.0
================================================================================
Loading required package: DBI
Platform design info loaded.
Reading in : /home/user/data/hugene21st/GSM1437906_GSM1437906_HTHuGene21_110512H_SL284_812407-2.CEL.gz
Mutating..
Joining..
Interesectiong..
Selecting..
docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/hugene21st Rscript convert.R -p hugene21st -o /home/user/data/out/ -i /home/user/data/hugene21st/GSM1437845_GSM1437845_HTHuGene21_102512H_SL228_810529-2.CEL.gz -d hugene21stprobeset -s hs -g GSM1437845_GSM1437845_HTHuGene21_102512H_SL228_810529-2
Loading required package: AnnotationDbi
Loading required package: methods
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: org.Hs.eg.db
Reading..
Loading required package: pd.hugene.2.1.st
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: RSQLite
Loading required package: oligoClasses
Welcome to oligoClasses version 1.40.0
Loading required package: oligo
================================================================================
Welcome to oligo version 1.42.0
================================================================================
Loading required package: DBI
Platform design info loaded.
Reading in : /home/user/data/hugene21st/GSM1437845_GSM1437845_HTHuGene21_102512H_SL228_810529-2.CEL.gz
Mutating..
Joining..
Interesectiong..
Selecting..
Ran a whole brain!
docker build -t convert/rhesus --build-arg package=pd.rhesus_3.12.0.tar.gz --build-arg db=rhesus -f Dockerfile.pd .
Sending build context to Docker daemon 3.904GB
Step 1/13 : FROM convert/base
---> d958adf36199
Step 2/13 : WORKDIR /home/user
---> Using cache
---> 47b27a4c2473
Step 3/13 : USER root
---> Using cache
---> c6cf6253bb3d
Step 4/13 : COPY install_pd.R .
---> Using cache
---> 0e591293bbac
Step 5/13 : ARG package
---> Using cache
---> 2a40e6020d31
Step 6/13 : ENV PACKAGE=$package
---> Running in 4e88e134b196
Removing intermediate container 4e88e134b196
---> a547fca2f81b
Step 7/13 : ARG db
---> Running in 28c7266736fd
Removing intermediate container 28c7266736fd
---> 5a8b6ae50e37
Step 8/13 : ENV DB=$db
---> Running in 48f84f7db410
Removing intermediate container 48f84f7db410
---> c13b5030e9f8
Step 9/13 : RUN Rscript install_pd.R
---> Running in 2856c748bfb4
Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help
A new version of Bioconductor is available after installing the most recent
version of R; see http://bioconductor.org/install
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15).
Installing package(s) 'rhesus.db'
Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv',
'spatial'
Warning message:
package 'rhesus.db' is not available (for R version 3.4.4)
Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.rhesus_3.12.0.tar.gz
Installing pd.rhesus
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
CMD INSTALL '/tmp/RtmpcZ8S9e/devtools73934c076/pd.rhesus' \
--library='/usr/local/lib/R/site-library' --install-tests
* installing *source* package 'pd.rhesus' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (pd.rhesus)
[[1]]
[1] TRUE
Removing intermediate container 2856c748bfb4
---> a36e41772c0e
Step 10/13 : VOLUME /home/user/data
---> Running in 5a7c8744a3c1
Removing intermediate container 5a7c8744a3c1
---> 151143f924e9
Step 11/13 : COPY convert.R .
---> 98cd34aa1a3e
Step 12/13 : USER user
---> Running in 62b49d6ab1c8
Removing intermediate container 62b49d6ab1c8
---> 52ea84f35fe0
Step 13/13 : ENTRYPOINT []
---> Running in b2823b49e8f1
Removing intermediate container b2823b49e8f1
---> de24f9e53371
Successfully built de24f9e53371
Successfully tagged convert/rhesus:latest
[Errno 2] No such file or directory: '/Users/rjones/Projects/gene-converter/cels/rhesus'
Ran a sample!
Ran a whole brain!
docker build -t convert/clariomsrat --build-arg package=pd.clariom.s.rat_3.14.1.tar.gz --build-arg db=clariomsrat -f Dockerfile.pd .
Sending build context to Docker daemon 3.904GB
Step 1/13 : FROM convert/base
---> d958adf36199
Step 2/13 : WORKDIR /home/user
---> Using cache
---> 47b27a4c2473
Step 3/13 : USER root
---> Using cache
---> c6cf6253bb3d
Step 4/13 : COPY install_pd.R .
---> Using cache
---> 0e591293bbac
Step 5/13 : ARG package
---> Using cache
---> 2a40e6020d31
Step 6/13 : ENV PACKAGE=$package
---> Running in 38548ac670c3
Removing intermediate container 38548ac670c3
---> c764e009537c
Step 7/13 : ARG db
---> Running in e738a4ffdbcb
Removing intermediate container e738a4ffdbcb
---> a0ca652577ce
Step 8/13 : ENV DB=$db
---> Running in ba27b247b78b
Removing intermediate container ba27b247b78b
---> 350bea7d1f12
Step 9/13 : RUN Rscript install_pd.R
---> Running in cbaa8e51ef22
Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help
A new version of Bioconductor is available after installing the most recent
version of R; see http://bioconductor.org/install
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15).
Installing package(s) 'clariomsrat.db'
Old packages: 'data.table', 'optparse', 'codetools', 'lattice', 'mgcv',
'spatial'
Warning message:
package 'clariomsrat.db' is not available (for R version 3.4.4)
Downloading package from url: https://bioconductor.org/packages/3.6/data/annotation/src/contrib/pd.clariom.s.rat_3.14.1.tar.gz
Installing pd.clariom.s.rat
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
CMD INSTALL '/tmp/RtmpKk3G2K/devtools722a76e7b/pd.clariom.s.rat' \
--library='/usr/local/lib/R/site-library' --install-tests
* installing *source* package 'pd.clariom.s.rat' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (pd.clariom.s.rat)
[[1]]
[1] TRUE
Removing intermediate container cbaa8e51ef22
---> 3dc1661b1f63
Step 10/13 : VOLUME /home/user/data
---> Running in f17ba760adc7
Removing intermediate container f17ba760adc7
---> 2e267d09d1be
Step 11/13 : COPY convert.R .
---> 0d9e0af98dee
Step 12/13 : USER user
---> Running in b947b569c706
Removing intermediate container b947b569c706
---> 506c625bd32b
Step 13/13 : ENTRYPOINT []
---> Running in cd4bda6d3edf
Removing intermediate container cd4bda6d3edf
---> 6c794f4250e6
Successfully built 6c794f4250e6
Successfully tagged convert/clariomsrat:latest
docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/clariomsrat Rscript convert.R -p clariomsrat -o /home/user/data/out/ -i /home/user/data/clariomsrat/GSM2479542_GSM2479542_kchip2shRNA2.CEL.gz -d clariomsrat -s rn -g GSM2479542_GSM2479542_kchip2shRNA2
Loading required package: AnnotationDbi
Loading required package: methods
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Error in library(db_package_name, character.only = TRUE) :
there is no package called 'clariomsrat.db'
Execution halted
docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/clariomsrat Rscript convert.R -p clariomsrat -o /home/user/data/out/ -i /home/user/data/clariomsrat/GSM2479540_GSM2479540_control3.CEL.gz -d clariomsrat -s rn -g GSM2479540_GSM2479540_control3
Loading required package: AnnotationDbi
Loading required package: methods
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Error in library(db_package_name, character.only = TRUE) :
there is no package called 'clariomsrat.db'
Execution halted
docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/clariomsrat Rscript convert.R -p clariomsrat -o /home/user/data/out/ -i /home/user/data/clariomsrat/GSM2479539_GSM2479539_control2.CEL.gz -d clariomsrat -s rn -g GSM2479539_GSM2479539_control2
Loading required package: AnnotationDbi
Loading required package: methods
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Error in library(db_package_name, character.only = TRUE) :
there is no package called 'clariomsrat.db'
Execution halted
docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/clariomsrat Rscript convert.R -p clariomsrat -o /home/user/data/out/ -i /home/user/data/clariomsrat/GSM2479541_GSM2479541_kchip2shRNA1.CEL.gz -d clariomsrat -s rn -g GSM2479541_GSM2479541_kchip2shRNA1
Loading required package: AnnotationDbi
Loading required package: methods
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Error in library(db_package_name, character.only = TRUE) :
there is no package called 'clariomsrat.db'
Execution halted
docker run -it -v /Users/rjones/Projects/gene-converter/cels:/home/user/data/ convert/clariomsrat Rscript convert.R -p clariomsrat -o /home/user/data/out/ -i /home/user/data/clariomsrat/GSM2479543_GSM2479543_kchip2shRNA3.CEL.gz -d clariomsrat -s rn -g GSM2479543_GSM2479543_kchip2shRNA3
Loading required package: AnnotationDbi
Loading required package: methods
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs