BioC 3.0: CHECK report for PGSEA on moscato1
This page was generated on 2015-04-10 09:44:41 -0700 (Fri, 10 Apr 2015).
PGSEA 1.40.0
Karl Dykema
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/PGSEA | | Last Changed Rev: 95439 / Revision: 102249 | | Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | OK | |
| moscato1 | Windows Server 2008 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
|
| Version: 1.40.0
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| Command: rm -rf PGSEA.buildbin-libdir PGSEA.Rcheck && mkdir PGSEA.buildbin-libdir PGSEA.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PGSEA.buildbin-libdir PGSEA_1.40.0.tar.gz >PGSEA.Rcheck\00install.out 2>&1 && cp PGSEA.Rcheck\00install.out PGSEA-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=PGSEA.buildbin-libdir --install="check:PGSEA-install.out" --force-multiarch --no-vignettes --timings PGSEA_1.40.0.tar.gz
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| StartedAt: 2015-04-10 04:06:31 -0700 (Fri, 10 Apr 2015)
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| EndedAt: 2015-04-10 04:11:23 -0700 (Fri, 10 Apr 2015)
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| EllapsedTime: 291.6 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:
###
### rm -rf PGSEA.buildbin-libdir PGSEA.Rcheck && mkdir PGSEA.buildbin-libdir PGSEA.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PGSEA.buildbin-libdir PGSEA_1.40.0.tar.gz >PGSEA.Rcheck\00install.out 2>&1 && cp PGSEA.Rcheck\00install.out PGSEA-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=PGSEA.buildbin-libdir --install="check:PGSEA-install.out" --force-multiarch --no-vignettes --timings PGSEA_1.40.0.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/PGSEA.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-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 '1.40.0'
* 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 ... 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
'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' ... [59s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
go2smc 47.18 0.68 47.87
** running examples for arch 'x64' ... [69s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
go2smc 56.28 0.79 57.08
* 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
NOTE: There were 2 notes.
See
'D:/biocbld/bbs-3.0-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_1.40.0.zip
* DONE (PGSEA)
PGSEA.Rcheck/examples_i386/PGSEA-Ex.timings:
| name | user | system | elapsed
|
| GOLUBmcs | 0.09 | 0.00 | 0.09 |
|
| PGSEA | 0.78 | 0.03 | 0.81 |
|
| VAIgsc | 1.12 | 0.07 | 1.19 |
|
| VAImcs | 0.24 | 0.00 | 0.23 |
|
| aggregateExprs | 0.39 | 0.00 | 1.39 |
|
| convertSmc | 0 | 0 | 0 |
|
| editSmc | 0.03 | 0.00 | 0.03 |
|
| go2smc | 47.18 | 0.68 | 47.87 |
|
| kegg2smc | 0.75 | 0.00 | 0.75 |
|
| nbEset | 0.14 | 0.03 | 0.18 |
|
| readGmt | 0.06 | 0.00 | 0.06 |
|
| readSmc | 0.05 | 0.02 | 0.06 |
|
| scanSmc | 0.03 | 0.00 | 0.03 |
|
| smcPlot | 0.76 | 0.00 | 0.77 |
|
| writeGmt | 0.06 | 0.00 | 0.06 |
|
| writeSmc | 0.07 | 0.00 | 0.06 |
|
PGSEA.Rcheck/examples_x64/PGSEA-Ex.timings:
| name | user | system | elapsed
|
| GOLUBmcs | 0.09 | 0.00 | 0.09 |
|
| PGSEA | 1.00 | 0.01 | 1.02 |
|
| VAIgsc | 1.21 | 0.05 | 1.26 |
|
| VAImcs | 0.27 | 0.00 | 0.27 |
|
| aggregateExprs | 0.39 | 0.05 | 0.43 |
|
| convertSmc | 0.02 | 0.00 | 0.02 |
|
| editSmc | 0.03 | 0.00 | 0.03 |
|
| go2smc | 56.28 | 0.79 | 57.08 |
|
| kegg2smc | 0.52 | 0.02 | 0.53 |
|
| nbEset | 0.12 | 0.00 | 0.13 |
|
| readGmt | 0.05 | 0.00 | 0.04 |
|
| readSmc | 0.04 | 0.00 | 0.05 |
|
| scanSmc | 0.02 | 0.00 | 0.02 |
|
| smcPlot | 0.47 | 0.00 | 0.46 |
|
| writeGmt | 0.08 | 0.00 | 0.08 |
|
| writeSmc | 0.06 | 0.00 | 0.06 |
|