PCpheno 1.32.0
Nolwenn Le Meur
| Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/PCpheno | | Last Changed Rev: 109589 / Revision: 116712 | | Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | [ WARNINGS ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### rm -rf PCpheno.buildbin-libdir PCpheno.Rcheck && mkdir PCpheno.buildbin-libdir PCpheno.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PCpheno.buildbin-libdir PCpheno_1.32.0.tar.gz >PCpheno.Rcheck\00install.out 2>&1 && cp PCpheno.Rcheck\00install.out PCpheno-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=PCpheno.buildbin-libdir --install="check:PCpheno-install.out" --force-multiarch --no-vignettes --timings PCpheno_1.32.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/PCpheno.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PCpheno/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PCpheno' version '1.32.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'Category' 'ScISI' 'SLGI' 'ppiStats' 'ppiData' 'annotate'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'PCpheno' can be installed ... WARNING
Found the following significant warnings:
Warning: package 'Matrix' was built under R version 3.2.5
See 'D:/biocbld/bbs-3.2-bioc/meat/PCpheno.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:
'Category' 'ScISI' 'KEGG.db' 'GO.db'
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 in package code:
'GO.db' 'KEGG.db'
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
'SLGI' 'annotate' 'ppiData' 'ppiStats'
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 ... OK
* 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' ... [51s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
gtResult-class 7.85 0.64 8.58
graphTheory 6.63 0.07 6.69
ppiInteraction 4.85 0.11 5.23
** running examples for arch 'x64' ... [43s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
graphTheory 7.93 0.21 8.13
gtResult-class 6.05 0.79 6.85
ppiInteraction 6.73 0.09 6.82
* 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
'D:/biocbld/bbs-3.2-bioc/meat/PCpheno.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'PCpheno' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: package 'Matrix' was built under R version 3.2.5
No methods found in "Biobase" for requests: listlen
No methods found in "annotate" for requests: pubmed, buildPubMedAbst
No methods found in "BiocGenerics" for requests: plot
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: package 'Matrix' was built under R version 3.2.5
No methods found in "Biobase" for requests: listlen
No methods found in "annotate" for requests: pubmed, buildPubMedAbst
No methods found in "BiocGenerics" for requests: plot
install for x64
* installing *source* package 'PCpheno' ...
** testing if installed package can be loaded
Warning: package 'Matrix' was built under R version 3.2.5
No methods found in "Biobase" for requests: listlen
No methods found in "annotate" for requests: pubmed, buildPubMedAbst
No methods found in "BiocGenerics" for requests: plot
* MD5 sums
packaged installation of 'PCpheno' as PCpheno_1.32.0.zip
* DONE (PCpheno)