Yang Cao
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/GeneExpressionSignature |
| Branch: RELEASE_3_12 |
| Last Commit: b183615 |
| Last Changed Date: 2020-10-27 10:42:35 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
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This page was generated on 2021-05-06 12:31:25 -0400 (Thu, 06 May 2021).
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To the developers/maintainers of the GeneExpressionSignature package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 686/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeneExpressionSignature 1.36.0 (landing page) Yang Cao
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: GeneExpressionSignature |
| Version: 1.36.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneExpressionSignature.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings GeneExpressionSignature_1.36.0.tar.gz |
| StartedAt: 2021-05-06 03:00:47 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 03:03:00 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 133.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: GeneExpressionSignature.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneExpressionSignature.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings GeneExpressionSignature_1.36.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/GeneExpressionSignature.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GeneExpressionSignature/DESCRIPTION' ... OK
* this is package 'GeneExpressionSignature' version '1.36.0'
* 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 'GeneExpressionSignature' can be installed ... WARNING
Found the following significant warnings:
Warning: Package 'KEGG.db' is deprecated and will be removed from Bioconductor
Warning: Package 'PGSEA' is deprecated and will be removed from Bioconductor
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/GeneExpressionSignature.Rcheck/00install.out' for details.
* 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 ... NOTE
Packages in Depends field not imported from:
'Biobase' 'PGSEA'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
RankMerging: no visible global function definition for 'exprs'
RankMerging: no visible global function definition for 'as'
RankMerging: no visible global function definition for 'phenoData'
RankMerging: no visible global function definition for 'new'
ScoreGSEA : PRL.Distance: no visible global function definition for
'exprs'
ScoreGSEA: no visible global function definition for 'exprs'
ScorePGSEA: no visible global function definition for 'exprs'
ScorePGSEA: no visible global function definition for 'new'
ScorePGSEA: no visible global function definition for 'PGSEA'
ScorePGSEA: no visible global function definition for 'pnorm'
getRLs : Check.Log: no visible global function definition for 'median'
integratePRL: no visible global function definition for 'phenoData'
integratePRL: no visible global function definition for 'exprs'
integratePRL: no visible global function definition for 'new'
integratePRL: no visible global function definition for 'as'
Undefined global functions or variables:
PGSEA as exprs median new phenoData pnorm
Consider adding
importFrom("methods", "as", "new")
importFrom("stats", "median", "pnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
SignatureDistance 5.87 0.03 5.91
ScoreGSEA 4.96 0.06 5.02
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
SignatureDistance 5.59 0.05 5.65
* 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: 1 WARNING, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/GeneExpressionSignature.Rcheck/00check.log'
for details.
GeneExpressionSignature.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/GeneExpressionSignature_1.36.0.tar.gz && rm -rf GeneExpressionSignature.buildbin-libdir && mkdir GeneExpressionSignature.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GeneExpressionSignature.buildbin-libdir GeneExpressionSignature_1.36.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL GeneExpressionSignature_1.36.0.zip && rm GeneExpressionSignature_1.36.0.tar.gz GeneExpressionSignature_1.36.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
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100 2326k 100 2326k 0 0 31.8M 0 --:--:-- --:--:-- --:--:-- 32.4M
install for i386
* installing *source* package 'GeneExpressionSignature' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning messages:
1: Package 'KEGG.db' is deprecated and will be removed from Bioconductor
version 3.12
2: Package 'PGSEA' is deprecated and will be removed from Bioconductor
version 3.13
** help
*** installing help indices
converting help for package 'GeneExpressionSignature'
finding HTML links ... done
GeneExpressionSignature html
RankMerging html
ScoreGSEA html
ScorePGSEA html
SignatureDistance html
exampleSet html
getRLs html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'KEGG.db' is deprecated and will be removed from Bioconductor
version 3.12
Warning: Package 'PGSEA' is deprecated and will be removed from Bioconductor
version 3.13
** testing if installed package can be loaded from final location
Warning: Package 'KEGG.db' is deprecated and will be removed from Bioconductor
version 3.12
Warning: Package 'PGSEA' is deprecated and will be removed from Bioconductor
version 3.13
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'GeneExpressionSignature' ...
** testing if installed package can be loaded
Warning: Package 'KEGG.db' is deprecated and will be removed from Bioconductor
version 3.12
Warning: Package 'PGSEA' is deprecated and will be removed from Bioconductor
version 3.13
* MD5 sums
packaged installation of 'GeneExpressionSignature' as GeneExpressionSignature_1.36.0.zip
* DONE (GeneExpressionSignature)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'GeneExpressionSignature' successfully unpacked and MD5 sums checked
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GeneExpressionSignature.Rcheck/examples_i386/GeneExpressionSignature-Ex.timings
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GeneExpressionSignature.Rcheck/examples_x64/GeneExpressionSignature-Ex.timings
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