macat 1.45.0
Joern Toedling
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/macat | | 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 | NotNeeded | OK | OK | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK | |
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### Running command:
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### rm -rf macat.buildbin-libdir macat.Rcheck && mkdir macat.buildbin-libdir macat.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=macat.buildbin-libdir macat_1.45.0.tar.gz >macat.Rcheck\00install.out 2>&1 && cp macat.Rcheck\00install.out macat-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=macat.buildbin-libdir --install="check:macat-install.out" --force-multiarch --no-vignettes --timings macat_1.45.0.tar.gz
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/macat.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 'macat/DESCRIPTION' ... OK
* this is package 'macat' version '1.45.0'
* 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 'macat' 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
** 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' call to 'annotate' which was already attached by Depends.
Please remove these calls from your code.
Packages in Depends field not imported from:
'Biobase' 'annotate'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: 'annotate:::getTDRows'
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
evalScoring : computePermSlideScores: warning in compute.sliding(permM,
chrom = chromosome, sample = 1, kernel, kernelparams, step.width =
step.width): partial argument match of 'chrom' to 'chromosome'
preprocessedLoader: warning in require(chip, character.only = TRUE,
quiet = TRUE): partial argument match of 'quiet' to 'quietly'
.onAttach: no visible global function definition for 'addVigs2WinMenu'
buildMACAT: no visible global function definition for 'featureNames'
buildMACAT: no visible global function definition for 'sampleNames'
buildMACAT: no visible global function definition for 'exprs'
preprocessedLoader: no visible global function definition for
'buildChromLocation'
preprocessedLoader: no visible global function definition for 'pData<-'
preprocessedLoader: no visible global function definition for
'varLabels<-'
preprocessedLoader: no visible global function definition for
'chromLocs'
preprocessedLoader : usedChromGenes2: no visible global function
definition for 'chromLocs'
preprocessedLoader : usedChromGenes2: no visible global function
definition for 'featureNames'
Undefined global functions or variables:
addVigs2WinMenu buildChromLocation chromLocs exprs featureNames
pData<- sampleNames varLabels<-
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [31s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
discretize_tscores 15.52 0.05 15.56
get_results 6.78 0.03 6.84
** running examples for arch 'x64' ... [46s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
discretize_tscores 23.61 0.09 23.70
get_results 11.33 0.00 11.33
* 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: 2 NOTEs
See
'c:/biocbld/bbs-3.3-bioc/meat/macat.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'macat' ...
** R
** data
** demo
** 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 'macat' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'macat' as macat_1.45.0.zip
* DONE (macat)