batpigandme/newlybroken_revdeps.md Secret

## newlybroken_revdeps.md

      
    Raw
  

              newlybroken_revdeps.md
            
          
    ActisoftR

Version: 0.0.1
Newly broken


checking examples ... ERROR
...
    intersect, setdiff, setequal, union

> library("lubridate")

Attaching package: ‘lubridate’

The following object is masked from ‘package:base’:

    date

> data(act)
> dat <- act %>% group_by(subject_ID) %>%
+   mutate(start = min(datime_start)) %>%
+   ungroup %>% filter(datime_start <= start + days(10), interval_type != "ACTIVE")
> plot_Darwent(dat,  acolor = c("#D55E00", "black", "#56B4E9"),
+                   tz2 = "Pacific/Auckland",
+                   si = c(4, 3, 2.5))
Error in manual_scale(aesthetics, values, ...) : 
  argument "values" is missing, with no default
Calls: plot_Darwent -> scale_fill_manual -> manual_scale -> force
Execution halted


checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
  ...
Warning: package 'dplyr' was built under R version 3.5.1
Quitting from lines 142-149 (ActisoftR.Rmd) 
Error: processing vignette 'ActisoftR.Rmd' failed with diagnostics:
argument "values" is missing, with no default
Execution halted


In both


checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.


AneuFinder

Version: 1.8.0
Newly broken


checking examples ... ERROR
...
> ### ** Examples
> 
> ## Get a BED file, bin it and run GC correction
> bedfile <- system.file("extdata", "KK150311_VI_07.bam.bed.gz", package="AneuFinderData")
> binned <- binReads(bedfile, assembly='mm10', binsize=1e6,
+                   chromosomes=c(1:19,'X','Y'))
Reading file KK150311_VI_07.bam.bed.gz ... 0.62s
Fetching chromosome lengths from UCSC ... 1.74s
Subsetting chromosomes ... 0.05s
Filtering reads ... 0.07s
Subsetting specified chromosomes ... 0.02s
Calculating complexity ... 0.2s
Removing duplicate reads ... 0.12s
Calculating coverage ... 0.5s
Making fixed-width bins for bin size 1e+06 ... 0.02s
Splitting into strands ... 0.02s
Counting overlaps for binsize_1e+06 ... 0.63s
> plot(binned[[1]], type=1)
Error in levels(dfplot.seg$state) : object 'dfplot.seg' not found
Calls: plot ... manual_scale -> force -> stateColors -> intersect -> levels
Execution halted


checking re-building of vignette outputs ... WARNING
...
     ## End(Not run)
     

Reading file hg19_diploid.bam.bed.gz ... 2.88s
Fetching chromosome lengths from UCSC ...Warning in FUN(genome = names(SUPPORTED_UCSC_GENOMES)[idx], circ_seqs = supported_genome$circ_seqs,  :
  NCBI seqlevel was set to NA for hg19 UCSC seqlevel(s) not in the NCBI assembly:
  chrM
 1.75s
Subsetting chromosomes ... 0.05s
Filtering reads ... 0.18s
Subsetting specified chromosomes ... 0.02s
Calculating complexity ... 1.1s
Removing duplicate reads ... 0.83s
Calculating coverage ... 0.41s
Making fixed-width bins for bin size 1e+05 ... 0.05s
Splitting into strands ... 0.01s
Counting overlaps for binsize_1e+05 ... 0.2s
Quitting from lines 110-132 (AneuFinder.Rnw) 
Error: processing vignette 'AneuFinder.Rnw' failed with diagnostics:
object 'dfplot.seg' not found
Execution halted


checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.


Newly fixed


R CMD check timed out

In both


checking whether package ‘AneuFinder’ can be installed ... WARNING
Found the following significant warnings:
  Warning: package ‘GenomicRanges’ was built under R version 3.5.1
  Warning: package ‘IRanges’ was built under R version 3.5.1
See ‘/Users/max/github/forks/ggplot2/revdep/checks.noindex/AneuFinder/new/AneuFinder.Rcheck/00install.out’ for details.


checking R code for possible problems ... NOTE
Aneufinder: multiple local function definitions for ‘parallel.helper’
  with different formal arguments


BloodCancerMultiOmics2017

Version: 1.0.2
Newly broken


checking re-building of vignette outputs ... WARNING
...

    discard

The following object is masked from 'package:readr':

    col_factor


Attaching package: 'xtable'

The following object is masked from 'package:ggdendro':

    label

Warning in has_utility("pdfcrop") :
  pdfcrop not installed or not in PATH
Quitting from lines 170-203 (./src/part01.Rmd) 
Quitting from lines 18-19 (./src/part01.Rmd) 
Error: processing vignette 'BloodCancerMultiOmics2017.Rmd' failed with diagnostics:
object '.all_aesthetics' not found
Execution halted


checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.


Newly fixed


R CMD check timed out

In both


checking installed package size ... NOTE
  installed size is 115.4Mb
  sub-directories of 1Mb or more:
    data     80.0Mb
    doc      26.5Mb
    extdata   8.5Mb


dartR

Version: 1.0.5
Newly broken


checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
  ...
R(67360,0x7fff8ce3a380) malloc: *** error for object 0x7fb927367ce0: incorrect checksum for freed object - object was probably modified after being freed.
*** set a breakpoint in malloc_error_break to debug


In both


checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.


checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  ‘DBI’ ‘Demerelate’ ‘misc3d’ ‘plotly’ ‘quadprog’ ‘rgl’
  All declared Imports should be used.


derfinderPlot

Version: 1.14.0
Newly broken


checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.


In both


R CMD check timed out


checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: 'RefManageR'
  All declared Imports should be used.


GenomicDataCommons

Version: 1.4.3
Newly broken


checking re-building of vignette outputs ... WARNING
...
Loading required package: magrittr

Attaching package: 'GenomicDataCommons'

The following object is masked from 'package:stats':

    filter

Quitting from lines 145-146 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
failed to rename downloaded file:

  from: '/Users/max/Library/Caches/GenomicDataCommons/581b0bcf-a7e5-44ec-818a-9193a0565095/.partial_download'
  to: '/Users/max/Library/Caches/GenomicDataCommons/581b0bcf-a7e5-44ec-818a-9193a0565095/347a8eeb-204f-41df-98d3-61394d2b7cd7.htseq.counts.gz'
  reason:
    cannot rename file
    '/Users/max/Library/Caches/GenomicDataCommons/581b0bcf-a7e5-44ec-818a-9193a0565095/.partial_download'
    to
    '/Users/max/Library/Caches/GenomicDataCommons/581b0bcf-a7e5-44ec-818a-9193a0565095/347a8eeb-204f-41df-98d3-61394d2b7cd7.htseq.counts.gz',
    reason 'No such file or directory'
Execution halted


Newly fixed


checking examples ... ERROR
...
> # get some example file uuids
> uuids <- files() %>%
+     filter(~ access == 'open' & file_size < 100000) %>%
+     results(size = 3) %>%
+     ids()
> 
> # and get the data, placing it into the gdc_cache() directory
> fpaths <- gdcdata(uuids, use_cached=TRUE)
Error in .gdc_file_rename(destfile, to, overwrite) : 
  failed to rename downloaded file:

  from: '/Users/max/Library/Caches/GenomicDataCommons/6f88847b-5643-4f79-96f0-79bec5e1ed33/.partial_download'
  to: '/Users/max/Library/Caches/GenomicDataCommons/6f88847b-5643-4f79-96f0-79bec5e1ed33/RIELS_p_TCGA_268_269_N_GenomeWideSNP_6_E12_1306390.nocnv_grch38.seg.v2.txt'
  reason:
    cannot rename file
    '/Users/max/Library/Caches/GenomicDataCommons/6f88847b-5643-4f79-96f0-79bec5e1ed33/.partial_download'
    to
    '/Users/max/Library/Caches/GenomicDataCommons/6f88847b-5643-4f79-96f0-79bec5e1ed33/RIELS_p_TCGA_268_269_N_GenomeWideSNP_6_E12_1306390.nocnv_grch38.seg.v2.txt',
    reason 'No such file or directory'
Calls: gdcdata -> mapply -> <Anonymous> -> .gdc_file_rename
Execution halted


In both


checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object '.htseq_importer'
  ‘fnames’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.


checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.


checking R code for possible problems ... NOTE
default_fields.character: no visible binding for global variable
  ‘defaults’
gdc_rnaseq: no visible binding for global variable ‘case_id’
gdc_rnaseq: no visible binding for global variable ‘file_id’
Undefined global functions or variables:
  case_id defaults file_id


ggmap

Version: 2.6.1
Newly broken


checking whether package ‘ggmap’ can be installed ... ERROR
Installation failed.
See ‘/Users/max/github/forks/ggplot2/revdep/checks.noindex/ggmap/new/ggmap.Rcheck/00install.out’ for details.


Newly fixed


checking examples ... ERROR
Running examples in ‘ggmap-Ex.R’ failed
The error most likely occurred in:

> ### Name: get_map
> ### Title: Grab a map.
> ### Aliases: get_map
> 
> ### ** Examples
> 
> map <- get_map()
Warning in download.file(url, destfile = tmp, quiet = !messaging, mode = "wb") :
  cannot open URL 'http://maps.googleapis.com/maps/api/staticmap?center=29.763284,-95.363271&zoom=10&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false': HTTP status was '403 Forbidden'
Error in download.file(url, destfile = tmp, quiet = !messaging, mode = "wb") : 
  cannot open URL 'http://maps.googleapis.com/maps/api/staticmap?center=29.763284,-95.363271&zoom=10&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false'
Calls: get_map -> get_googlemap -> download.file
Execution halted


checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.


Installation

Devel

* installing *source* package ‘ggmap’ ...
** package ‘ggmap’ successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Error in get(".all_aesthetics", envir = asNamespace("ggplot2")) : 
  object '.all_aesthetics' not found
Error : unable to load R code in package ‘ggmap’
ERROR: lazy loading failed for package ‘ggmap’
* removing ‘/Users/max/github/forks/ggplot2/revdep/checks.noindex/ggmap/new/ggmap.Rcheck/ggmap’


CRAN

* installing *source* package ‘ggmap’ ...
** package ‘ggmap’ successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (ggmap)


ggridges

Version: 0.5.0
Newly broken


checking examples ... ERROR
...
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library(ggplot2)

Attaching package: ‘ggplot2’

The following object is masked from ‘package:ggridges’:

    scale_discrete_manual

> 
> # default jittered points
> ggplot(iris, aes(x = Sepal.Length, y = Species)) +
+   geom_density_ridges(jittered_points = TRUE, position = "points_jitter", alpha = 0.7)
Picking joint bandwidth of 0.181
Error in col[, rep(1, length(alpha)), drop = FALSE] : 
  subscript out of bounds
Calls: <Anonymous> ... grob -> <Anonymous> -> validGP -> numnotnull -> alpha
Execution halted


checking re-building of vignette outputs ... WARNING
...

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Picking joint bandwidth of 3.16
Warning: Removed 6 rows containing non-finite values (stat_density_ridges).
Loading required package: viridisLite
Picking joint bandwidth of 3.37
Loading required package: lattice
Picking joint bandwidth of 2.8
Quitting from lines 108-127 (gallery.Rmd) 
Error: processing vignette 'gallery.Rmd' failed with diagnostics:
subscript out of bounds
Execution halted


In both


checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.


checking data for non-ASCII characters ... NOTE
  Note: found 6242 marked UTF-8 strings


ggtern

Version: 3.0.0
Newly broken


checking whether package ‘ggtern’ can be installed ... ERROR
Installation failed.
See ‘/Users/max/github/forks/ggplot2/revdep/checks.noindex/ggtern/new/ggtern.Rcheck/00install.out’ for details.


Newly fixed


checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.


checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘chemometrics’


Installation

Devel

* installing *source* package ‘ggtern’ ...
** package ‘ggtern’ successfully unpacked and MD5 sums checked
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
Error in get(x, envir = ns, inherits = FALSE) : 
  object '.element_tree' not found
Error : unable to load R code in package ‘ggtern’
ERROR: lazy loading failed for package ‘ggtern’
* removing ‘/Users/max/github/forks/ggplot2/revdep/checks.noindex/ggtern/new/ggtern.Rcheck/ggtern’


CRAN

* installing *source* package ‘ggtern’ ...
** package ‘ggtern’ successfully unpacked and MD5 sums checked
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (ggtern)


gifski

Version: 0.8.3
Newly broken


checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.


Newly fixed


checking whether package ‘gifski’ can be installed ... ERROR
Installation failed.
See ‘/Users/max/github/forks/ggplot2/revdep/checks.noindex/gifski/old/gifski.Rcheck/00install.out’ for details.


Installation

Devel

* installing *source* package ‘gifski’ ...
** package ‘gifski’ successfully unpacked and MD5 sums checked
info: downloading installer
info: syncing channel updates for 'stable-x86_64-apple-darwin'
info: latest update on 2018-09-25, rust version 1.29.1 (b801ae664 2018-09-20)
info: downloading component 'rustc'
info: downloading component 'rust-std'
info: downloading component 'cargo'
info: downloading component 'rust-docs'
info: installing component 'rustc'
info: installing component 'rust-std'
info: installing component 'cargo'
info: installing component 'rust-docs'
info: default toolchain set to 'stable'

  stable installed - rustc 1.29.1 (b801ae664 2018-09-20)


Rust is installed now. Great!

To get started you need Cargo's bin directory ($HOME/.cargo/bin) in your PATH 
environment variable. Next time you log in this will be done automatically.

To configure your current shell run source $HOME/.cargo/env
** libs
rm -Rf gifski.so myrustlib/target/release/libmyrustlib.a wrapper.o myrustlib/target
/usr/local/clang4/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -pthread -fPIC  -Wall -g -O2  -c wrapper.c -o wrapper.o
/Users/max/.cargo/bin/cargo build --release --manifest-path=myrustlib/Cargo.toml
    Updating registry `https://github.com/rust-lang/crates.io-index`
 Downloading gifski v0.8.3
 Downloading gif-dispose v2.1.0
 Downloading clap v2.31.2
 Downloading error-chain v0.11.0
 Downloading imagequant v2.11.9
 Downloading rayon v0.9.0
 Downloading rgb v0.8.7
 Downloading imgref v1.3.4
 Downloading resize v0.3.0
 Downloading lodepng v2.1.5
 Downloading wild v0.1.1
 Downloading gif v0.9.2
 Downloading pbr v1.0.0
 Downloading glob v0.2.11
 Downloading lzw v0.10.0
 Downloading color_quant v1.0.0
 Downloading strsim v0.7.0
 Downloading textwrap v0.9.0
 Downloading bitflags v1.0.3
 Downloading ansi_term v0.11.0
 Downloading vec_map v0.8.0
 Downloading atty v0.2.10
 Downloading unicode-width v0.1.4
 Downloading libc v0.2.40
 Downloading backtrace v0.3.7
 Downloading rustc-demangle v0.1.8
 Downloading cfg-if v0.1.3
 Downloading imagequant-sys v2.11.9
 Downloading cc v1.0.15
 Downloading rayon-core v1.4.0
 Downloading either v1.5.0
 Downloading num_cpus v1.8.0
 Downloading rand v0.4.2
 Downloading lazy_static v1.0.0
 Downloading crossbeam-deque v0.2.0
 Downloading crossbeam-epoch v0.3.1
 Downloading crossbeam-utils v0.2.2
 Downloading scopeguard v0.3.3
 Downloading memoffset v0.2.1
 Downloading nodrop v0.1.12
 Downloading arrayvec v0.4.7
 Downloading time v0.1.39
 Downloading winapi v0.2.8
 Downloading kernel32-sys v0.2.2
 Downloading winapi-build v0.1.1
   Compiling nodrop v0.1.12
   Compiling cfg-if v0.1.3
   Compiling scopeguard v0.3.3
   Compiling winapi-build v0.1.1
   Compiling lazy_static v1.0.0
   Compiling cc v1.0.15
   Compiling memoffset v0.2.1
   Compiling rayon-core v1.4.0
   Compiling libc v0.2.40
   Compiling rustc-demangle v0.1.8
   Compiling color_quant v1.0.0
   Compiling rgb v0.8.7
   Compiling unicode-width v0.1.4
   Compiling lzw v0.10.0
   Compiling winapi v0.2.8
   Compiling either v1.5.0
   Compiling imgref v1.3.4
   Compiling vec_map v0.8.0
   Compiling strsim v0.7.0
   Compiling ansi_term v0.11.0
   Compiling bitflags v1.0.3
   Compiling glob v0.2.11
   Compiling resize v0.3.0
   Compiling wild v0.1.1
   Compiling crossbeam-utils v0.2.2
   Compiling arrayvec v0.4.7
   Compiling kernel32-sys v0.2.2
   Compiling num_cpus v1.8.0
   Compiling rand v0.4.2
   Compiling time v0.1.39
   Compiling atty v0.2.10
   Compiling lodepng v2.1.5
   Compiling backtrace v0.3.7
   Compiling textwrap v0.9.0
   Compiling gif v0.9.2
   Compiling imagequant-sys v2.11.9
   Compiling crossbeam-epoch v0.3.1
   Compiling error-chain v0.11.0
   Compiling clap v2.31.2
   Compiling gif-dispose v2.1.0
   Compiling crossbeam-deque v0.2.0
   Compiling pbr v1.0.0
   Compiling imagequant v2.11.9
   Compiling rayon v0.9.0
   Compiling gifski v0.8.3
   Compiling myrustlib v0.1.0 (file:///Users/max/github/forks/ggplot2/revdep/checks.noindex/gifski/new/gifski.Rcheck/00_pkg_src/gifski/src/myrustlib)
    Finished release [optimized] target(s) in 2m 58s
/usr/local/clang4/bin/clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/clang4/lib -o gifski.so wrapper.o -Lmyrustlib/target/release -lmyrustlib -lresolv -pthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
clang-4.0: warning: argument unused during compilation: '-pthread' [-Wunused-command-line-argument]
ld: warning: text-based stub file /System/Library/Frameworks//CoreFoundation.framework/CoreFoundation.tbd and library file /System/Library/Frameworks//CoreFoundation.framework/CoreFoundation are out of sync. Falling back to library file for linking.
installing to /Users/max/github/forks/ggplot2/revdep/checks.noindex/gifski/new/gifski.Rcheck/gifski/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (gifski)


CRAN

* installing *source* package ‘gifski’ ...
** package ‘gifski’ successfully unpacked and MD5 sums checked
info: downloading installer
info: syncing channel updates for 'stable-x86_64-apple-darwin'
info: latest update on 2018-09-25, rust version 1.29.1 (b801ae664 2018-09-20)
info: downloading component 'rustc'
error: component download failed for rustc-x86_64-apple-darwin
info: caused by: could not rename downloaded file from '/Users/max/.rustup/downloads/3f7289db7a5c64f96c4debb25885927ecfa5a98c8825e1874cc9a7da547e9e3e.partial' to '/Users/max/.rustup/downloads/3f7289db7a5c64f96c4debb25885927ecfa5a98c8825e1874cc9a7da547e9e3e'
info: caused by: No such file or directory (os error 2)
** libs
rm -Rf gifski.so myrustlib/target/release/libmyrustlib.a wrapper.o myrustlib/target
/usr/local/clang4/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -pthread -fPIC  -Wall -g -O2  -c wrapper.c -o wrapper.o
/Users/max/.cargo/bin/cargo build --release --manifest-path=myrustlib/Cargo.toml
error: no default toolchain configured
make: *** [myrustlib/target/release/libmyrustlib.a] Error 1
make: *** Waiting for unfinished jobs....
ERROR: compilation failed for package ‘gifski’
* removing ‘/Users/max/github/forks/ggplot2/revdep/checks.noindex/gifski/old/gifski.Rcheck/gifski’


GOexpress

Version: 1.14.0
Newly broken


checking installed package size ... NOTE
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.3Mb


In both


checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.


checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.


checking R code for possible problems ... NOTE
GO_analyse: no visible binding for global variable ‘microarray2dataset’
GO_analyse: no visible binding for global variable ‘prefix2dataset’
mart_from_ensembl: no visible binding for global variable
  ‘prefix2dataset’
Undefined global functions or variables:
  microarray2dataset prefix2dataset


checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘VennDiagram’


checking re-building of vignette outputs ... NOTE
...
  There are other near singularities as well. 1783.4
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,  :
  pseudoinverse used at 1.77
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,  :
  neighborhood radius 22.23
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,  :
  reciprocal condition number  1.3784e-16
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,  :
  There are other near singularities as well. 1783.4
Warning in predLoess(object$y, object$x, newx = if (is.null(newdata)) object$x else if (is.data.frame(newdata)) as.matrix(model.frame(delete.response(terms(object)),  :
  pseudoinverse used at 1.77
Warning in predLoess(object$y, object$x, newx = if (is.null(newdata)) object$x else if (is.data.frame(newdata)) as.matrix(model.frame(delete.response(terms(object)),  :
  neighborhood radius 22.23
Warning in predLoess(object$y, object$x, newx = if (is.null(newdata)) object$x else if (is.data.frame(newdata)) as.matrix(model.frame(delete.response(terms(object)),  :
  reciprocal condition number  1.3784e-16
Warning in predLoess(object$y, object$x, newx = if (is.null(newdata)) object$x else if (is.data.frame(newdata)) as.matrix(model.frame(delete.response(terms(object)),  :
  There are other near singularities as well. 1783.4
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'GOexpress-UsersGuide.tex' failed.
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted


MCbiclust

Version: 1.4.0
Newly broken


checking examples ... ERROR
...
> data(CCLE_small)
> data(Mitochondrial_genes)
> 
> mito.loc <- (row.names(CCLE_small) %in% Mitochondrial_genes)
> CCLE.mito <- CCLE_small[mito.loc,]
> 
> set.seed(102)
> CCLE.seed <- FindSeed(gem = CCLE.mito,
+                       seed.size = 10,
+                       iterations = 100,
+                       messages = 1000)
Iteration	Correlation Score
> 
> CCLE.sort <- SampleSort(gem = CCLE.mito,seed = CCLE.seed,sort.length = 11)
Sort Length 	 Cor Score
Warning in socketConnection(port = port, server = TRUE, blocking = TRUE,  :
  port 11488 cannot be opened
Error in socketConnection(port = port, server = TRUE, blocking = TRUE,  : 
  cannot open the connection
Calls: SampleSort ... <Anonymous> -> <Anonymous> -> newSOCKnode -> socketConnection
Execution halted


In both


checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.


checking installed package size ... NOTE
  installed size is  9.9Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    5.9Mb


mglR

Version: 0.1.0
Newly broken


checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.


Newly fixed


R CMD check timed out

PTXQC

Version: 0.92.3
Newly broken


R CMD check timed out

Newly fixed


checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.


In both


checking installed package size ... NOTE
  installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc        4.6Mb
    examples   2.2Mb


RITAN

Version: 1.4.2
Newly broken


checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.


Newly fixed


R CMD check timed out

In both


checking Rd \usage sections ... WARNING
Documented arguments not in \usage in documentation object 'resource_reduce':
  ‘mutual_overlap’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.


checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘sqldf’
A package should be listed in only one of these fields.


checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  ‘BgeeDB’ ‘dynamicTreeCut’ ‘gsubfn’
  All declared Imports should be used.


checking R code for possible problems ... NOTE
...
load_geneset_symbols: no visible binding for global variable
  ‘geneset_list’
load_geneset_symbols: no visible binding for global variable ‘f’
load_geneset_symbols: no visible binding for global variable
  ‘active_genesets’
network_overlap : <anonymous>: no visible binding for global variable
  ‘network_list’
network_overlap: no visible binding for global variable ‘network_list’
network_overlap : select_edges: no visible binding for global variable
  ‘network_list’
plot.term_enrichment_by_subset: no visible binding for global variable
  ‘Var2’
plot.term_enrichment_by_subset: no visible binding for global variable
  ‘Var1’
show_active_genesets_hist: no visible binding for global variable
  ‘active_genesets’
term_enrichment : process_source: no visible binding for global
  variable ‘active_genesets’
Undefined global functions or variables:
  Var1 Var2 active_genesets all_net all_symbols f geneset_list
  network_list ss2


scDD

Version: 1.4.0
Newly broken


checking examples ... ERROR
...
> ### ** Examples
> 
>  
> # load toy simulated example SingleCellExperiment object to find DD genes  
> data(scDatExSim)
> 
> # set arguments to pass to scDD function
> 
> prior_param=list(alpha=0.01, mu0=0, s0=0.01, a0=0.01, b0=0.01)
> 
> # call the scDD function to perform permutations and classify DD genes
> 
> scDatExSim <- scDD(scDatExSim, prior_param=prior_param, testZeroes=FALSE)
Setting up parallel back-end using 18 cores
Clustering observed expression data for each gene
Warning in socketConnection(host, port, TRUE, TRUE, "a+b", timeout = timeout) :
  port 11229 cannot be opened
Error in socketConnection(host, port, TRUE, TRUE, "a+b", timeout = timeout) : 
  cannot open the connection
Calls: scDD ... .local -> .bpfork -> .bpforkConnect -> socketConnection
Execution halted


In both


checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
  ...
Warning in has_utility("pdfcrop") :
  pdfcrop not installed or not in PATH

Attaching package: 'gridExtra'

The following object is masked from 'package:Biobase':

    combine

The following object is masked from 'package:BiocGenerics':

    combine

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'scDD.tex' failed.
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted


checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.


checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  ‘grDevices’ ‘graphics’ ‘stats’
  All declared Imports should be used.


checking R code for possible problems ... NOTE
...
  ‘binomial’
validation : <anonymous>: no visible global function definition for
  ‘var’
validation: no visible binding for global variable ‘var’
validation: no visible global function definition for ‘par’
validation: no visible global function definition for ‘plot’
validation: no visible global function definition for ‘abline’
validation: no visible global function definition for ‘points’
Undefined global functions or variables:
  abline axis binomial density dev.off fisher.test hcl hist ks.test
  lines lm model.matrix p.adjust par pchisq pdf plot points quantile
  rbinom rect residuals rnbinom rt runif t.test var
Consider adding
  importFrom("grDevices", "dev.off", "hcl", "pdf")
  importFrom("graphics", "abline", "axis", "hist", "lines", "par",
             "plot", "points", "rect")
  importFrom("stats", "binomial", "density", "fisher.test", "ks.test",
             "lm", "model.matrix", "p.adjust", "pchisq", "quantile",
             "rbinom", "residuals", "rnbinom", "rt", "runif", "t.test",
             "var")
to your NAMESPACE file.


seqsetvis

Version: 1.0.2
Newly broken


checking examples ... ERROR
Running examples in ‘seqsetvis-Ex.R’ failed
The error most likely occurred in:

> ### Name: ssvSignalBandedQuantiles
> ### Title: plot profiles from bigwigs
> ### Aliases: ssvSignalBandedQuantiles
> 
> ### ** Examples
> 
> #rainbow colors
> ssvSignalBandedQuantiles(CTCF_in_10a_profiles_gr)
Error in manual_scale(aesthetics, values, ...) : 
  argument "values" is missing, with no default
Calls: ssvSignalBandedQuantiles -> scale_color_manual -> manual_scale -> force
Execution halted


checking tests ...
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  argument "values" is missing, with no default
  1: ssvSignalBandedQuantiles(test_object, by_ = "sample", hsv_reverse = T) at testthat/test_ssvSignalPlots.R:17
  2: scale_color_manual(breaks = q2do, palette = cols)
  3: manual_scale(aesthetics, values, ...)
  4: force(values)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 817 SKIPPED: 0 FAILED: 4
  1. Error: ssvSignalBandedQuantiles works with proper inputs (@test_ssvSignalPlots.R#10) 
  2. Error: ssvSignalBandedQuantiles different hsv setting (@test_ssvSignalPlots.R#17) 
  3. Error: ssvSignalBandedQuantiles works with proper inputs (@test_ssvSignalPlots.R#10) 
  4. Error: ssvSignalBandedQuantiles different hsv setting (@test_ssvSignalPlots.R#17) 
  
  Error: testthat unit tests failed
  Execution halted


checking re-building of vignette outputs ... WARNING
...
The following object is masked from 'package:IRanges':

    shift

The following objects are masked from 'package:S4Vectors':

    first, second


Attaching package: 'cowplot'

The following object is masked from 'package:ggplot2':

    ggsave

convert: profile 'icc': 'RGB ': RGB color space not permitted on grayscale PNG `seqsetvis_overview_files/figure-html/binary heatmap-1.png' @ warning/png.c/MagickPNGWarningHandler/1744.
convert: profile 'icc': 'RGB ': RGB color space not permitted on grayscale PNG `seqsetvis_overview_files/figure-html/scatterplot basic-1.png' @ warning/png.c/MagickPNGWarningHandler/1744.
Quitting from lines 371-374 (seqsetvis_overview.Rmd) 
Error: processing vignette 'seqsetvis_overview.Rmd' failed with diagnostics:
argument "values" is missing, with no default
Execution halted


In both


checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.


shadowtext

Version: 0.0.2
Newly broken


checking examples ... ERROR
Running examples in ‘shadowtext-Ex.R’ failed
The error most likely occurred in:

> ### Name: geom_shadowtext
> ### Title: geom_shadowtext
> ### Aliases: geom_shadowtext
> 
> ### ** Examples
> 
> library(ggplot2)
> d <- data.frame(x = rnorm(3), y=rnorm(3), label = c('hello', 'world', '!!!'))
> ggplot(d, aes(x,y)) + geom_shadowtext(aes(label=label, color=label), bgcolor='firebrick')
Error in col[, rep(1, length(alpha)), drop = FALSE] : 
  subscript out of bounds
Calls: <Anonymous> ... do.call -> <Anonymous> -> f -> shadowtextGrob -> alpha
Execution halted


checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
  ...
Quitting from lines 52-75 (shadowtext.Rmd) 
Error: processing vignette 'shadowtext.Rmd' failed with diagnostics:
subscript out of bounds
Execution halted


In both


checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.


tricolore

Version: 1.2.0
Newly broken


checking examples ... ERROR
Running examples in ‘tricolore-Ex.R’ failed
The error most likely occurred in:

> ### Name: ColorKeySextant
> ### Title: Sextant Scheme Legend
> ### Aliases: ColorKeySextant
> ### Keywords: internal
> 
> ### ** Examples
> 
> tricolore:::ColorKeySextant(center = prop.table(runif(3)),
+                            values = c('#01A0C6', '#B8B3D8', '#F11D8C',
+                                       '#FFB3B3', '#FFFF00', '#B3DCC3'),
+                            label_as = 'pct_diff', show_center = TRUE)
Error in get(x, envir = ns, inherits = FALSE) : 
  object '.all_aesthetics' not found
Calls: <Anonymous> ... geom_Lline -> aes -> rename_aes -> getFromNamespace -> get
Execution halted


In both


checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.


checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.


checking data for non-ASCII characters ... NOTE
  Note: found 88 marked UTF-8 strings


tsbox

Version: 0.0.3
Newly broken


checking tests ...
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
     })
  7: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
         e$call <- cl.i
         stop(e)
     })
  8: tryCatchList(expr, classes, parentenv, handlers)
  9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  10: value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 346 SKIPPED: 10 FAILED: 1
  1. Error: colname guessing works as expected (@test_ts_pc.R#25) 
  
  Error: testthat unit tests failed
  Execution halted


In both


checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.