Aditya Bhagwat
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/autonomics |
| git_branch: RELEASE_3_13 |
| git_last_commit: 5df16f7 |
| git_last_commit_date: 2021-05-25 07:57:21 -0400 (Tue, 25 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:05:58 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the autonomics package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/autonomics.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 102/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| autonomics 1.0.1 (landing page) Aditya Bhagwat
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: autonomics |
| Version: 1.0.1 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:autonomics.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings autonomics_1.0.1.tar.gz |
| StartedAt: 2021-10-14 19:43:37 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 20:00:30 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 1013.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: autonomics.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:autonomics.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings autonomics_1.0.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/autonomics.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'autonomics/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'autonomics' version '1.0.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'autonomics' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
'translate'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'autonomics-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: read_affymetrix
> ### Title: Read affymetrix microarray
> ### Aliases: read_affymetrix
>
> ### ** Examples
>
> require(magrittr)
Loading required package: magrittr
> url <- paste0('http://www.bioconductor.org/help/publications/2003/',
+ 'Chiaretti/chiaretti2/T33.tgz')
> localfile <- file.path('~/autonomicscache', basename(url))
> if (!file.exists(localfile)){
+ download.file(url, destfile = localfile)
+ untar(localfile, exdir = path.expand('~/autonomicscache'))
+ }
Error in download.file(url, destfile = localfile) :
cannot open destfile '~/autonomicscache/T33.tgz', reason 'No such file or directory'
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'autonomics-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: read_affymetrix
> ### Title: Read affymetrix microarray
> ### Aliases: read_affymetrix
>
> ### ** Examples
>
> require(magrittr)
Loading required package: magrittr
> url <- paste0('http://www.bioconductor.org/help/publications/2003/',
+ 'Chiaretti/chiaretti2/T33.tgz')
> localfile <- file.path('~/autonomicscache', basename(url))
> if (!file.exists(localfile)){
+ download.file(url, destfile = localfile)
+ untar(localfile, exdir = path.expand('~/autonomicscache'))
+ }
Error in download.file(url, destfile = localfile) :
cannot open destfile '~/autonomicscache/T33.tgz', reason 'No such file or directory'
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 1 WARNING, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/autonomics.Rcheck/00check.log'
for details.
autonomics.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/autonomics_1.0.1.tar.gz && rm -rf autonomics.buildbin-libdir && mkdir autonomics.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=autonomics.buildbin-libdir autonomics_1.0.1.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL autonomics_1.0.1.zip && rm autonomics_1.0.1.tar.gz autonomics_1.0.1.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
2 9411k 2 222k 0 0 723k 0 0:00:13 --:--:-- 0:00:13 723k
46 9411k 46 4409k 0 0 3416k 0 0:00:02 0:00:01 0:00:01 3415k
100 9411k 100 9411k 0 0 4202k 0 0:00:02 0:00:02 --:--:-- 4205k
install for i386
* installing *source* package 'autonomics' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Note: wrong number of arguments to '/'
** help
*** installing help indices
converting help for package 'autonomics'
finding HTML links ... done
AUTONOMICS_DATASETS html
MAXQUANT_PATTERNS_PEPCOUNTS html
MAXQUANT_PATTERNS_QUANTITY html
TESTS html
add_smiles html
analysis html
analyze html
assert_is_valid_sumexp html
biplot html
biplot_corrections html
biplot_covariates html
center html
contrast_subgroup_cols html
contrastdefs html
counts html
counts2cpm html
counts2tpm html
cpm html
create_design html
create_sfile html
default_formula html
default_sfile html
download_data html
download_gtf html
dt2mat html
explore_imputations html
explore_transformations html
extract_features html
extract_rectangle html
fdata html
filter_exprs_replicated_in_some_subgroup
html
filter_features html
filter_medoid html
filter_replicated html
filter_samples html
fit_limma html
flevels html
fnames html
formula2str html
fvalues html
fvars html
guess_maxquant_quantity html
guess_sep html
halfnormimpute html
impute_systematic_nondetects html
invert html
is_imputed html
is_sig html
limma html
log2counts html
log2countsratios html
log2cpm html
log2cpmratios html
log2tpm html
log2tpmratios html
log2transform html
make_volcano_dt html
matrix2sumexp html
merge_sdata html
merge_sfile html
message_df html
occupancies html
pca html
plot_boxplots html
plot_contrastogram html
plot_data html
plot_densities html
plot_detections html
plot_features html
plot_venn html
plot_violins html
plot_volcano html
preprocess_rnaseq_counts html
proteingroups html
read_affymetrix html
read_metabolon html
read_proteingroups html
read_rectangles html
read_rnaseq_counts html
read_somascan html
rm_singleton_samples html
scaledlibsizes html
sdata html
slevels html
snames html
split_by_svar html
split_extract html
standardize_maxquant_snames html
subgroup_matrix html
subtract_baseline html
sumexp2mae html
sumexp_to_long_dt html
summarize_fit html
svalues html
svars html
tpm html
values html
venn_detects html
weights html
zero_to_na html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'autonomics' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'autonomics' as autonomics_1.0.1.zip
* DONE (autonomics)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'autonomics' successfully unpacked and MD5 sums checked
|
autonomics.Rcheck/tests_i386/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
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.
> library(testthat)
> library(autonomics)
Attaching package: 'autonomics'
The following object is masked from 'package:stats':
biplot
>
> test_check("autonomics")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 102 ]
>
> proc.time()
user system elapsed
122.37 4.37 124.75
|
autonomics.Rcheck/tests_x64/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
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.
> library(testthat)
> library(autonomics)
Attaching package: 'autonomics'
The following object is masked from 'package:stats':
biplot
>
> test_check("autonomics")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 102 ]
>
> proc.time()
user system elapsed
126.70 2.75 127.70
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autonomics.Rcheck/examples_i386/autonomics-Ex.timings
|
autonomics.Rcheck/examples_x64/autonomics-Ex.timings
|