BioC 2.14: CHECK report for annaffy on moscato2
This page was generated on 2014-10-08 08:50:42 -0700 (Wed, 08 Oct 2014).
annaffy 1.36.0 Colin A. Smith
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/annaffy | Last Changed Rev: 88838 / Revision: 95116 | Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | OK | |
moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ OK ] | OK |
petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK |
morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK |
Summary
Package: annaffy
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Version: 1.36.0
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Command: rm -rf annaffy.buildbin-libdir && mkdir annaffy.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=annaffy.buildbin-libdir annaffy_1.36.0.tar.gz >annaffy-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=annaffy.buildbin-libdir --install="check:annaffy-install.out" --force-multiarch --no-vignettes --timings annaffy_1.36.0.tar.gz
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StartedAt: 2014-10-07 22:37:24 -0700 (Tue, 07 Oct 2014)
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EndedAt: 2014-10-07 22:39:47 -0700 (Tue, 07 Oct 2014)
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EllapsedTime: 143.6 seconds
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RetCode: 0
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Status: OK
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CheckDir: annaffy.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 annaffy.buildbin-libdir && mkdir annaffy.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=annaffy.buildbin-libdir annaffy_1.36.0.tar.gz >annaffy-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=annaffy.buildbin-libdir --install="check:annaffy-install.out" --force-multiarch --no-vignettes --timings annaffy_1.36.0.tar.gz
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* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/annaffy.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'annaffy/DESCRIPTION' ... OK
* this is package 'annaffy' 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 'annaffy' 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' call to 'methods' which was already attached by Depends.
Please remove these calls from your code.
Packages in Depends field not imported from:
'GO.db' 'KEGG.db' 'methods'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
Missing object imported by a ':::' call: 'Biobase:::biocReposList'
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* 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' ... [13s] OK
** running examples for arch 'x64' ... [9s] OK
* 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
NOTE: There was 1 note.
See
'E:/biocbld/bbs-2.14-bioc/meat/annaffy.Rcheck/00check.log'
for details.
annaffy.Rcheck/00install.out:
install for i386
* installing *source* package 'annaffy' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'colnames<-' from package 'base' in package 'annaffy'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'annaffy' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'annaffy' as annaffy_1.36.0.zip
* DONE (annaffy)
annaffy.Rcheck/examples_i386/annaffy-Ex.timings:
name | user | system | elapsed
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aafChromLoc | 0.52 | 0.03 | 0.54 |
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aafChromosome | 0.06 | 0.02 | 0.08 |
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aafCytoband | 0.09 | 0.00 | 0.28 |
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aafDescription | 0.07 | 0.00 | 0.07 |
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aafGO | 0.66 | 0.00 | 0.66 |
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aafGenBank | 0.08 | 0.00 | 0.23 |
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aafLocusLink | 0.07 | 0.00 | 0.08 |
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aafPathway | 0.75 | 0.01 | 0.89 |
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aafProbe | 0.06 | 0.00 | 0.06 |
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aafPubMed | 0.19 | 0.00 | 2.65 |
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aafSearchText | 1.19 | 0.02 | 1.20 |
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aafSymbol | 0.07 | 0.00 | 0.06 |
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aafUniGene | 0.07 | 0.00 | 0.19 |
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is.annpkg | 0.81 | 0.17 | 0.98 |
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annaffy.Rcheck/examples_x64/annaffy-Ex.timings:
name | user | system | elapsed
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aafChromLoc | 0.47 | 0.01 | 0.49 |
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aafChromosome | 0.08 | 0.00 | 0.07 |
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aafCytoband | 0.07 | 0.02 | 0.08 |
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aafDescription | 0.04 | 0.01 | 0.06 |
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aafGO | 0.74 | 0.00 | 0.73 |
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aafGenBank | 0.07 | 0.00 | 0.08 |
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aafLocusLink | 0.05 | 0.02 | 0.06 |
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aafPathway | 0.84 | 0.03 | 0.87 |
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aafProbe | 0.03 | 0.01 | 0.05 |
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aafPubMed | 0.15 | 0.00 | 0.15 |
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aafSearchText | 1.33 | 0.02 | 1.34 |
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aafSymbol | 0.07 | 0.00 | 0.06 |
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aafUniGene | 0.04 | 0.02 | 0.06 |
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is.annpkg | 0.75 | 0.14 | 0.89 |
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