attract 1.22.0
Jessica Mar
| Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/attract | | Last Changed Rev: 109589 / Revision: 109947 | | Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015) |
| linux1.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| windows1.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ WARNINGS ] | OK | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | WARNINGS | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | OK | |
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### Running command:
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### rm -rf attract.buildbin-libdir attract.Rcheck && mkdir attract.buildbin-libdir attract.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=attract.buildbin-libdir attract_1.22.0.tar.gz >attract.Rcheck\00install.out 2>&1 && cp attract.Rcheck\00install.out attract-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=attract.buildbin-libdir --install="check:attract-install.out" --force-multiarch --no-vignettes --timings attract_1.22.0.tar.gz
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* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/attract.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'attract/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'attract' version '1.22.0'
* 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 'attract' can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import by 'AnnotationDbi::makeGOGraph' when loading 'attract'
See 'C:/biocbld/bbs-3.2-bioc/meat/attract.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
'AnnotationDbi' 'KEGG.db' 'limma' 'cluster' 'GOstats' 'graphics' 'methods' 'stats'
A package should be listed in only one of these fields.
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
'GOstats' 'KEGG.db' 'cluster' 'limma'
Please remove these calls from your code.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotsynexprs: warning in axis(1, at = tickMarks, lab = tickLabels):
partial argument match of 'lab' to 'labels'
removeFlatGenes: warning in topTable(fit2, coef =
(1:(length(my.contrasts))), adjust = "fdr", n = nrow(dat.fr)):
partial argument match of 'n' to 'number'
removeFlatGenes: warning in topTable(fit2, coef =
(1:(length(my.contrasts))), adjust = "fdr", n = nrow(dat.fr)):
partial argument match of 'adjust' to 'adjust.method'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [26s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
findCorrPartners 7.63 0.22 7.84
findAttractors 6.31 0.09 7.21
findSynexprs 5.95 0.05 6.00
** running examples for arch 'x64' ... [28s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
findCorrPartners 8.06 0.08 8.14
findAttractors 7.20 0.06 7.27
findSynexprs 6.63 0.01 6.64
* 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, 3 NOTEs
See
'C:/biocbld/bbs-3.2-bioc/meat/attract.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'attract' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import by 'AnnotationDbi::makeGOGraph' when loading 'attract'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by 'AnnotationDbi::makeGOGraph' when loading 'attract'
install for x64
* installing *source* package 'attract' ...
** testing if installed package can be loaded
Warning: replacing previous import by 'AnnotationDbi::makeGOGraph' when loading 'attract'
* MD5 sums
packaged installation of 'attract' as attract_1.22.0.zip
* DONE (attract)