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lcolladotor/install_log_BiocManager.txt

Created November 30, 2018 19:42
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Windows installation problems for GO.db that is needed by clusterProfiler
Raw
install_log_BiocManager.txt
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
[Previously saved workspace restored]
> BiocManager::install("GO.db")
Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.0 (2018-04-23)
Installing package(s) 'GO.db'
installing the source package ‘GO.db’
trying URL 'https://bioconductor.org/packages/3.8/data/annotation/src/contrib/GO.db_3.7.0.tar.gz'
Content type 'application/x-gzip' length 31820876 bytes (30.3 MB)
downloaded 30.3 MB
Error in untar2(tarfile, files, list, exdir, restore_times) :
incomplete block on file
In R CMD INSTALL
The downloaded source packages are in
‘C:\Users\Richard Straub\AppData\Local\Temp\RtmpUhCid7\downloaded_packages’
Update old packages: 'BiocParallel', 'GenomeInfoDbData', 'rcmdcheck'
Update all/some/none? [a/s/n]: n
Warning message:
In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
installation of package ‘GO.db’ had non-zero exit status
> traceback()
No traceback available
> options(width = 120)
> sessioninfo::session_info()
- Session info -------------------------------------------------------------------------------------------------------
setting value
version R version 3.5.0 (2018-04-23)
os Windows 10 x64
system x86_64, mingw32
ui Rgui
language (EN)
collate English_United States.1252
ctype English_United States.1252
tz America/New_York
date 2018-11-30
- Packages -----------------------------------------------------------------------------------------------------------
package * version date lib source
assertthat 0.2.0 2017-04-11 [1] CRAN (R 3.5.0)
BiocManager 1.30.4 2018-11-13 [1] CRAN (R 3.5.1)
cli 1.0.1 2018-09-25 [1] CRAN (R 3.5.1)
crayon 1.3.4 2017-09-16 [1] CRAN (R 3.5.0)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.5.1)
withr 2.1.2 2018-03-15 [1] CRAN (R 3.5.0)
[1] C:/Users/Richard Straub/Documents/R/win-library/3.5
[2] C:/Program Files/R/R-3.5.0/library
Raw
install_log_uncompressed_on_macOS.txt
Microsoft Windows [Version 10.0.17134.407]
(c) 2018 Microsoft Corporation. All rights reserved.
C:\Users\Richard Straub>cd Desktop
C:\Users\Richard Straub\Desktop>cd GO.db
C:\Users\Richard Straub\Desktop\GO.db>R CMD INSTALL .
In R CMD INSTALL
* installing to library 'C:/Users/Richard Straub/Documents/R/win-library/3.5'
* installing *source* package 'GO.db' ...
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: package 'AnnotationDbi' was built under R version 3.5.1
Warning: package 'BiocGenerics' was built under R version 3.5.1
Warning: package 'Biobase' was built under R version 3.5.1
Warning: package 'IRanges' was built under R version 3.5.1
Warning: package 'S4Vectors' was built under R version 3.5.1
** help
*** installing help indices
converting help for package 'GO.db'
finding HTML links ... done
GOBASE html
GOBPANCESTOR html
GOBPCHILDREN html
GOBPOFFSPRING html
GOBPPARENTS html
GOCCANCESTOR html
GOCCCHILDREN html
GOCCOFFSPRING html
GOCCPARENTS html
GOMAPCOUNTS html
GOMFANCESTOR html
GOMFCHILDREN html
GOMFOFFSPRING html
GOMFPARENTS html
GOOBSOLETE html
GOSYNONYM html
GOTERM html
GO_dbconn html
** building package indices
** testing if installed package can be loaded
*** arch - i386
ARGUMENT 'Straub\AppData\Local\Temp\RtmpqYI4Uh\Rin50f46ad41dfa' __ignored__
Error: object 'ÿ_' not found
Execution halted
*** arch - x64
ARGUMENT 'Straub\AppData\Local\Temp\RtmpqYI4Uh\Rin50f43f76d75' __ignored__
Error: object 'ÿ_' not found
Execution halted
ERROR: loading failed for 'i386', 'x64'
* removing 'C:/Users/Richard Straub/Documents/R/win-library/3.5/GO.db'
C:\Users\Richard Straub\Desktop\GO.db>
Raw
load_log_post_installation_EB_BiocManager.txt
The downloaded source packages are in
'C:\Users\eburke10\AppData\Local\Temp\RtmpkH8oes\downloaded_packages'
installation path not writeable, unable to update packages: foreign, lattice,
MASS, Matrix, mgcv, survival
> library(clusterProfiler)
clusterProfiler v3.10.0 For help: https://guangchuangyu.github.io/software/clusterProfiler
If you use clusterProfiler in published research, please cite:
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287.
>
>
>
> install.packages("sessioninfo")
Installing package into 'C:/Users/eburke10/Documents/R/win-library/3.5'
(as 'lib' is unspecified)
trying URL 'https://cloud.r-project.org/bin/windows/contrib/3.5/sessioninfo_1.1.1.zip'
Content type 'application/zip' length 46408 bytes (45 KB)
downloaded 45 KB
package 'sessioninfo' successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\eburke10\AppData\Local\Temp\RtmpkH8oes\downloaded_packages
> options(width=120)
> sessioninfo::session_info()
- Session info -------------------------------------------------------------------------------------------------------
setting value
version R version 3.5.1 (2018-07-02)
os Windows 10 x64
system x86_64, mingw32
ui RTerm
language (EN)
collate English_United States.1252
ctype English_United States.1252
tz America/New_York
date 2018-11-30
- Packages -----------------------------------------------------------------------------------------------------------
package * version date lib source
AnnotationDbi 1.44.0 2018-10-30 [1] Bioconductor
assertthat 0.2.0 2017-04-11 [1] CRAN (R 3.5.1)
bindr 0.1.1 2018-03-13 [1] CRAN (R 3.5.1)
bindrcpp 0.2.2 2018-03-29 [1] CRAN (R 3.5.1)
Biobase 2.42.0 2018-10-30 [1] Bioconductor
BiocGenerics 0.28.0 2018-10-30 [1] Bioconductor
BiocManager 1.30.4 2018-11-13 [1] CRAN (R 3.5.1)
BiocParallel 1.16.2 2018-11-28 [1] Bioconductor
bit 1.1-14 2018-05-29 [1] CRAN (R 3.5.0)
bit64 0.9-7 2017-05-08 [1] CRAN (R 3.5.0)
blob 1.1.1 2018-03-25 [1] CRAN (R 3.5.1)
cli 1.0.1 2018-09-25 [1] CRAN (R 3.5.1)
clusterProfiler * 3.10.0 2018-10-30 [1] Bioconductor
colorspace 1.3-2 2016-12-14 [1] CRAN (R 3.5.1)
cowplot 0.9.3 2018-07-15 [1] CRAN (R 3.5.1)
crayon 1.3.4 2017-09-16 [1] CRAN (R 3.5.1)
data.table 1.11.8 2018-09-30 [1] CRAN (R 3.5.1)
DBI 1.0.0 2018-05-02 [1] CRAN (R 3.5.1)
digest 0.6.18 2018-10-10 [1] CRAN (R 3.5.1)
DO.db 2.9 2018-11-30 [1] Bioconductor
DOSE 3.8.0 2018-10-30 [1] Bioconductor
dplyr 0.7.8 2018-11-10 [1] CRAN (R 3.5.1)
enrichplot 1.2.0 2018-10-30 [1] Bioconductor
europepmc 0.3 2018-04-20 [1] CRAN (R 3.5.1)
farver 1.1.0 2018-11-20 [1] CRAN (R 3.5.1)
fastmatch 1.1-0 2017-01-28 [1] CRAN (R 3.5.0)
fgsea 1.8.0 2018-10-31 [1] Bioconductor
ggforce 0.1.3 2018-07-07 [1] CRAN (R 3.5.1)
ggplot2 3.1.0 2018-10-25 [1] CRAN (R 3.5.1)
ggplotify 0.0.3 2018-08-03 [1] CRAN (R 3.5.1)
ggraph 1.0.2 2018-07-07 [1] CRAN (R 3.5.1)
ggrepel 0.8.0 2018-05-09 [1] CRAN (R 3.5.1)
ggridges 0.5.1 2018-09-27 [1] CRAN (R 3.5.1)
glue 1.3.0 2018-07-17 [1] CRAN (R 3.5.1)
GO.db 3.7.0 2018-11-30 [1] Bioconductor
GOSemSim 2.8.0 2018-10-30 [1] Bioconductor
gridExtra 2.3 2017-09-09 [1] CRAN (R 3.5.1)
gridGraphics 0.3-0 2018-04-03 [1] CRAN (R 3.5.1)
gtable 0.2.0 2016-02-26 [1] CRAN (R 3.5.1)
hms 0.4.2 2018-03-10 [1] CRAN (R 3.5.1)
httr 1.3.1 2017-08-20 [1] CRAN (R 3.5.1)
igraph 1.2.2 2018-07-27 [1] CRAN (R 3.5.1)
IRanges 2.16.0 2018-10-30 [1] Bioconductor
jsonlite 1.5 2017-06-01 [1] CRAN (R 3.5.1)
lattice 0.20-35 2017-03-25 [2] CRAN (R 3.5.1)
lazyeval 0.2.1 2017-10-29 [1] CRAN (R 3.5.1)
magrittr 1.5 2014-11-22 [1] CRAN (R 3.5.1)
MASS 7.3-50 2018-04-30 [2] CRAN (R 3.5.1)
Matrix 1.2-14 2018-04-13 [2] CRAN (R 3.5.1)
memoise 1.1.0 2017-04-21 [1] CRAN (R 3.5.1)
munsell 0.5.0 2018-06-12 [1] CRAN (R 3.5.1)
pillar 1.3.0 2018-07-14 [1] CRAN (R 3.5.1)
pkgconfig 2.0.2 2018-08-16 [1] CRAN (R 3.5.1)
plyr 1.8.4 2016-06-08 [1] CRAN (R 3.5.1)
prettyunits 1.0.2 2015-07-13 [1] CRAN (R 3.5.1)
progress 1.2.0 2018-06-14 [1] CRAN (R 3.5.1)
purrr 0.2.5 2018-05-29 [1] CRAN (R 3.5.1)
qvalue 2.14.0 2018-10-30 [1] Bioconductor
R6 2.3.0 2018-10-04 [1] CRAN (R 3.5.1)
RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 3.5.0)
Rcpp 1.0.0 2018-11-07 [1] CRAN (R 3.5.1)
reshape2 1.4.3 2017-12-11 [1] CRAN (R 3.5.1)
rlang 0.3.0.1 2018-10-25 [1] CRAN (R 3.5.1)
RSQLite 2.1.1 2018-05-06 [1] CRAN (R 3.5.1)
rvcheck 0.1.1 2018-09-27 [1] CRAN (R 3.5.1)
S4Vectors 0.20.1 2018-11-09 [1] Bioconductor
scales 1.0.0 2018-08-09 [1] CRAN (R 3.5.1)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.5.1)
stringi 1.2.4 2018-07-20 [1] CRAN (R 3.5.1)
stringr 1.3.1 2018-05-10 [1] CRAN (R 3.5.1)
tibble 1.4.2 2018-01-22 [1] CRAN (R 3.5.1)
tidyr 0.8.2 2018-10-28 [1] CRAN (R 3.5.1)
tidyselect 0.2.5 2018-10-11 [1] CRAN (R 3.5.1)
triebeard 0.3.0 2016-08-04 [1] CRAN (R 3.5.1)
tweenr 1.0.0 2018-09-27 [1] CRAN (R 3.5.1)
units 0.6-1 2018-09-21 [1] CRAN (R 3.5.1)
UpSetR 1.3.3 2017-03-21 [1] CRAN (R 3.5.1)
urltools 1.7.1 2018-08-03 [1] CRAN (R 3.5.1)
viridis 0.5.1 2018-03-29 [1] CRAN (R 3.5.1)
viridisLite 0.3.0 2018-02-01 [1] CRAN (R 3.5.1)
withr 2.1.2 2018-03-15 [1] CRAN (R 3.5.1)
xml2 1.2.0 2018-01-24 [1] CRAN (R 3.5.1)
[1] C:/Users/eburke10/Documents/R/win-library/3.5
[2] C:/Program Files/R/R-3.5.1/library
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