BioC 3.2: CHECK report for PGSEA on windows1.bioconductor.org
This page was generated on 2015-10-27 17:28:19 -0400 (Tue, 27 Oct 2015).
PGSEA 1.44.0 Karl Dykema
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/PGSEA | 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 | OK | OK | OK | |  |
windows1.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ OK ] | OK |  |
perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK |  |
oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK |  |
Summary
Package: PGSEA
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Version: 1.44.0
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Command: rm -rf PGSEA.buildbin-libdir PGSEA.Rcheck && mkdir PGSEA.buildbin-libdir PGSEA.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PGSEA.buildbin-libdir PGSEA_1.44.0.tar.gz >PGSEA.Rcheck\00install.out 2>&1 && cp PGSEA.Rcheck\00install.out PGSEA-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=PGSEA.buildbin-libdir --install="check:PGSEA-install.out" --force-multiarch --no-vignettes --timings PGSEA_1.44.0.tar.gz
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StartedAt: 2015-10-27 04:24:15 -0400 (Tue, 27 Oct 2015)
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EndedAt: 2015-10-27 04:27:01 -0400 (Tue, 27 Oct 2015)
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EllapsedTime: 166.2 seconds
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RetCode: 0
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Status: OK
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CheckDir: PGSEA.Rcheck
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Warnings: 0
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Command output
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### Running command:
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### rm -rf PGSEA.buildbin-libdir PGSEA.Rcheck && mkdir PGSEA.buildbin-libdir PGSEA.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PGSEA.buildbin-libdir PGSEA_1.44.0.tar.gz >PGSEA.Rcheck\00install.out 2>&1 && cp PGSEA.Rcheck\00install.out PGSEA-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=PGSEA.buildbin-libdir --install="check:PGSEA-install.out" --force-multiarch --no-vignettes --timings PGSEA_1.44.0.tar.gz
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* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/PGSEA.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 'PGSEA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PGSEA' version '1.44.0'
* 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 'PGSEA' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
'library' or 'require' calls to packages already attached by Depends:
'GO.db' 'KEGG.db'
Please remove these calls from your code.
'library' or 'require' call to 'org.Hs.eg.db' in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
'GO.db' 'KEGG.db' 'annaffy' 'methods'
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
aggregateExprs: warning in mget(ids, env = Env, ifnotfound = NA):
partial argument match of 'env' to 'envir'
go2smc: no visible binding for global variable 'GOTERM'
go2smc: no visible binding for global variable 'org.Hs.egGO2ALLEGS'
kegg2smc: no visible binding for global variable 'KEGGPATHNAME2ID'
kegg2smc: no visible binding for global variable 'KEGGPATHID2EXTID'
* 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' ... [37s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
go2smc 31.14 0.83 31.97
** running examples for arch 'x64' ... [45s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
go2smc 39 0.9 39.9
* 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: 3 NOTEs
See
'C:/biocbld/bbs-3.2-bioc/meat/PGSEA.Rcheck/00check.log'
for details.
PGSEA.Rcheck/00install.out:
install for i386
* installing *source* package 'PGSEA' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'PGSEA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PGSEA' as PGSEA_1.44.0.zip
* DONE (PGSEA)
PGSEA.Rcheck/examples_i386/PGSEA-Ex.timings:
name | user | system | elapsed
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GOLUBmcs | 0.08 | 0.00 | 0.08 |
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PGSEA | 0.39 | 0.03 | 0.42 |
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VAIgsc | 0.51 | 0.03 | 0.54 |
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VAImcs | 0.17 | 0.00 | 0.17 |
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aggregateExprs | 0.20 | 0.03 | 0.24 |
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convertSmc | 0 | 0 | 0 |
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editSmc | 0.02 | 0.00 | 0.02 |
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go2smc | 31.14 | 0.83 | 31.97 |
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kegg2smc | 0.31 | 0.00 | 0.31 |
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nbEset | 0.09 | 0.00 | 0.09 |
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readGmt | 0.03 | 0.00 | 0.03 |
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readSmc | 0.04 | 0.00 | 0.04 |
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scanSmc | 0.01 | 0.00 | 0.01 |
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smcPlot | 0.25 | 0.09 | 0.34 |
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writeGmt | 0.02 | 0.02 | 0.04 |
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writeSmc | 0.01 | 0.02 | 0.03 |
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PGSEA.Rcheck/examples_x64/PGSEA-Ex.timings:
name | user | system | elapsed
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GOLUBmcs | 0.07 | 0.00 | 0.06 |
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PGSEA | 0.42 | 0.00 | 0.42 |
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VAIgsc | 0.53 | 0.05 | 0.58 |
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VAImcs | 0.21 | 0.01 | 0.24 |
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aggregateExprs | 0.29 | 0.00 | 0.28 |
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convertSmc | 0 | 0 | 0 |
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editSmc | 0.01 | 0.00 | 0.02 |
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go2smc | 39.0 | 0.9 | 39.9 |
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kegg2smc | 0.30 | 0.01 | 0.31 |
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nbEset | 0.08 | 0.02 | 0.10 |
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readGmt | 0.04 | 0.00 | 0.04 |
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readSmc | 0.03 | 0.00 | 0.04 |
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scanSmc | 0.02 | 0.00 | 0.01 |
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smcPlot | 0.3 | 0.0 | 0.3 |
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writeGmt | 0.03 | 0.00 | 0.03 |
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writeSmc | 0.08 | 0.00 | 0.08 |
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