BioC 3.3: CHECK report for GOstats on windows2.bioconductor.org
This page was generated on 2015-10-27 12:13:58 -0400 (Tue, 27 Oct 2015).
GOstats 2.37.0
Bioconductor Package Maintainer
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GOstats | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ OK ] | OK | |
Summary
| Package: GOstats
|
| Version: 2.37.0
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| Command: rm -rf GOstats.buildbin-libdir GOstats.Rcheck && mkdir GOstats.buildbin-libdir GOstats.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GOstats.buildbin-libdir GOstats_2.37.0.tar.gz >GOstats.Rcheck\00install.out 2>&1 && cp GOstats.Rcheck\00install.out GOstats-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=GOstats.buildbin-libdir --install="check:GOstats-install.out" --force-multiarch --no-vignettes --timings GOstats_2.37.0.tar.gz
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| StartedAt: 2015-10-27 02:55:30 -0400 (Tue, 27 Oct 2015)
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| EndedAt: 2015-10-27 02:59:05 -0400 (Tue, 27 Oct 2015)
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| EllapsedTime: 215.1 seconds
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| RetCode: 0
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| Status: OK
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| CheckDir: GOstats.Rcheck
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| Warnings: 0
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Command output
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### Running command:
###
### rm -rf GOstats.buildbin-libdir GOstats.Rcheck && mkdir GOstats.buildbin-libdir GOstats.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GOstats.buildbin-libdir GOstats_2.37.0.tar.gz >GOstats.Rcheck\00install.out 2>&1 && cp GOstats.Rcheck\00install.out GOstats-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=GOstats.buildbin-libdir --install="check:GOstats-install.out" --force-multiarch --no-vignettes --timings GOstats_2.37.0.tar.gz
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/GOstats.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GOstats/DESCRIPTION' ... OK
* this is package 'GOstats' version '2.37.0'
* 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 'GOstats' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
'Biobase' 'Category' 'graph' 'GO.db' 'annotate'
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
* 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 in package code:
'Rgraphviz' 'SparseM'
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported object imported by a ':::' call: 'Category:::XXX_getSummaryGeneric_XXX'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
compCorrGraph: no visible global function definition for
'as.matrix.csr'
plotGOTermGraph: no visible global function definition for
'makeNodeAttrs'
Undefined global functions or variables:
as.matrix.csr makeNodeAttrs
* 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' ... [11s] OK
** running examples for arch 'x64' ... [12s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R' [32s]
[32s] OK
** running tests for arch 'x64' ...
Running 'runTests.R' [34s]
[34s] 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
* DONE
Status: 3 NOTEs
See
'c:/biocbld/bbs-3.3-bioc/meat/GOstats.Rcheck/00check.log'
for details.
GOstats.Rcheck/00install.out:
install for i386
* installing *source* package 'GOstats' ...
** 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 'GOstats' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GOstats' as GOstats_2.37.0.zip
* DONE (GOstats)
GOstats.Rcheck/examples_i386/GOstats-Ex.timings:
| name | user | system | elapsed
|
| Ndists | 0.06 | 0.00 | 0.07 |
|
| compCorrGraph | 0.12 | 0.00 | 0.12 |
|
| compGdist | 0.08 | 0.00 | 0.07 |
|
| idx2dimnames | 0.03 | 0.00 | 0.04 |
|
| makeGOGraph | 1.12 | 0.08 | 1.20 |
|
| notConn | 0.02 | 0.00 | 0.01 |
|
| oneGOGraph | 0.34 | 0.00 | 0.35 |
|
| probeSetSummary | 1.56 | 0.10 | 1.65 |
|
| shortestPath | 2.64 | 0.01 | 2.66 |
|
| simLL | 0.67 | 0.00 | 0.67 |
|
| triadCensus | 0 | 0 | 0 |
|
GOstats.Rcheck/examples_x64/GOstats-Ex.timings:
| name | user | system | elapsed
|
| Ndists | 0.04 | 0.00 | 0.05 |
|
| compCorrGraph | 0.14 | 0.00 | 0.14 |
|
| compGdist | 0.09 | 0.00 | 0.10 |
|
| idx2dimnames | 0.02 | 0.00 | 0.01 |
|
| makeGOGraph | 1.54 | 0.03 | 1.57 |
|
| notConn | 0.03 | 0.00 | 0.04 |
|
| oneGOGraph | 0.38 | 0.00 | 0.37 |
|
| probeSetSummary | 2.23 | 0.10 | 2.33 |
|
| shortestPath | 2.66 | 0.00 | 2.66 |
|
| simLL | 0.64 | 0.00 | 0.64 |
|
| triadCensus | 0 | 0 | 0 |
|