Julien Wollbrett
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/BgeeCall |
| git_branch: RELEASE_3_13 |
| git_last_commit: 75b35d9 |
| git_last_commit_date: 2021-05-19 12:48:49 -0400 (Wed, 19 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 BgeeCall package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BgeeCall.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 142/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BgeeCall 1.8.0 (landing page) Julien Wollbrett
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: BgeeCall |
| Version: 1.8.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BgeeCall.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings BgeeCall_1.8.0.tar.gz |
| StartedAt: 2021-10-14 20:01:35 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 20:10:01 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 505.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BgeeCall.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BgeeCall.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings BgeeCall_1.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/BgeeCall.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 'BgeeCall/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BgeeCall' version '1.8.0'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'BgeeCall' can be installed ... OK
* checking installed package size ... NOTE
installed size is 9.3Mb
sub-directories of 1Mb or more:
extdata 8.6Mb
* 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 ... NOTE
approachesMerging : <anonymous>: no visible global function definition
for 'p.adjust'
generate_calls_workflow: no visible binding for global variable
'myUserMetadata'
generate_qValue: no visible global function definition for 'approxfun'
generate_qValue: no visible global function definition for 'integrate'
generate_qValue : calculate_qValue: no visible global function
definition for 'integrate'
generate_theoretical_pValue: no visible binding for global variable
'abundance'
generate_theoretical_pValue: no visible binding for global variable
'type'
generate_theoretical_pValue: no visible global function definition for
'pnorm'
merging_libraries: no visible binding for global variable 'read.delim'
should_ignore_tx_version: no visible global function definition for
'complete.cases'
Undefined global functions or variables:
abundance approxfun complete.cases integrate myUserMetadata p.adjust
pnorm read.delim type
Consider adding
importFrom("stats", "approxfun", "complete.cases", "integrate",
"p.adjust", "pnorm")
importFrom("utils", "read.delim")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* 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' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
generate_presence_absence 5.53 0.44 14.55
setAnnotationFromFile 2.62 1.09 5.11
merge_transcriptome_and_intergenic 0.85 0.10 9.59
list_bgee_ref_intergenic_species 0.01 0.02 8.17
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
generate_presence_absence 4.58 0.13 7.38
list_bgee_ref_intergenic_species 0.02 0.06 7.73
* 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 NOTEs
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/BgeeCall.Rcheck/00check.log'
for details.
BgeeCall.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/BgeeCall_1.8.0.tar.gz && rm -rf BgeeCall.buildbin-libdir && mkdir BgeeCall.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BgeeCall.buildbin-libdir BgeeCall_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL BgeeCall_1.8.0.zip && rm BgeeCall_1.8.0.tar.gz BgeeCall_1.8.0.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
14 5798k 14 816k 0 0 2070k 0 0:00:02 --:--:-- 0:00:02 2071k
92 5798k 92 5380k 0 0 3817k 0 0:00:01 0:00:01 --:--:-- 3818k
100 5798k 100 5798k 0 0 3904k 0 0:00:01 0:00:01 --:--:-- 3904k
install for i386
* installing *source* package 'BgeeCall' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'BgeeCall'
finding HTML links ... done
AbundanceMetadata-class html
BgeeCall html
BgeeMetadata-class html
KallistoMetadata-class html
UserMetadata-class html
create_kallisto_index html
download_fasta_intergenic html
download_kallisto html
generate_calls_workflow html
generate_presence_absence html
generate_slurm_calls html
generate_slurm_indexes html
getIntergenicPrefix html
getIntergenicRelease html
getRunIds html
getSimpleArborescence html
getWorkingPath html
get_summary_stats html
list_bgee_ref_intergenic_species html
list_community_ref_intergenic_species html
list_intergenic_release html
merge_transcriptome_and_intergenic html
merging_libraries html
run_kallisto html
run_tximport html
setAnnotationFromFile html
setAnnotationFromObject html
setIntergenicRelease html
setOutputDir html
setRNASeqLibPath html
setRunIds html
setSimpleArborescence html
setTranscriptomeFromFile html
setTranscriptomeFromObject html
setWorkingPath 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 'BgeeCall' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BgeeCall' as BgeeCall_1.8.0.zip
* DONE (BgeeCall)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'BgeeCall' successfully unpacked and MD5 sums checked
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BgeeCall.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(BgeeCall)
>
> Sys.setenv("R_TESTS" = "")
> test_check("BgeeCall")
trying URL 'ftp://ftp.bgee.org/intergenic/0.1/ref_intergenic/6239_intergenic.fa.gz'
length 4420457 bytes (4.2 MB)
==================================================
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 15 ]
>
> proc.time()
user system elapsed
28.14 2.65 52.31
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BgeeCall.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(BgeeCall)
>
> Sys.setenv("R_TESTS" = "")
> test_check("BgeeCall")
trying URL 'https://github.com/pachterlab/kallisto/releases/download/v0.45.0/kallisto_windows-v0.45.0.zip'
Content type 'application/octet-stream' length 4387130 bytes (4.2 MB)
==================================================
downloaded 4.2 MB
trying URL 'ftp://ftp.bgee.org/intergenic/0.1/ref_intergenic/6239_intergenic.fa.gz'
length 4420457 bytes (4.2 MB)
==================================================
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 15 ]
>
> proc.time()
user system elapsed
28.67 1.75 53.48
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BgeeCall.Rcheck/examples_i386/BgeeCall-Ex.timings
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BgeeCall.Rcheck/examples_x64/BgeeCall-Ex.timings
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