Joern Toedling
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/macat |
| Branch: RELEASE_3_9 |
| Last Commit: 337acb7 |
| Last Changed Date: 2019-05-02 11:53:03 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:19:44 -0400 (Wed, 16 Oct 2019).
| Package 900/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| macat 1.58.0 Joern Toedling
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: macat |
| Version: 1.58.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:macat.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings macat_1.58.0.tar.gz |
| StartedAt: 2019-10-16 04:52:23 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 04:55:03 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 159.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: macat.Rcheck |
| Warnings: 2 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:macat.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings macat_1.58.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/macat.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.58.0'
* 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 ... WARNING
Found the following significant warnings:
Warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6rtDdB/R.INSTALL124c3f324a76/macat/man/loaddatapkg.Rd:24: unexpected '}'
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/macat.Rcheck/00install.out' for details.
* 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 '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'
compare.gammas: no visible global function definition for 'x11'
compare.gammas: no visible global function definition for 'lines'
compare.gammas: no visible global function definition for 'legend'
discreteKernelize: no visible binding for global variable 'quantile'
discretize: no visible binding for global variable 'quantile'
discretizeChromosome: no visible binding for global variable 'quantile'
discretizeOne: no visible binding for global variable 'quantile'
evalScoring: no visible binding for global variable 'quantile'
getHtml: no visible global function definition for 'browseURL'
loaddatapkg: no visible global function definition for
'install.packages'
loaddatapkg: no visible global function definition for 'contrib.url'
plot.MACATevalScoring: no visible global function definition for 'x11'
plot.MACATevalScoring: no visible global function definition for 'png'
plot.MACATevalScoring: no visible global function definition for 'par'
plot.MACATevalScoring: no visible global function definition for
'points'
plot.MACATevalScoring: no visible global function definition for
'lines'
plot.MACATevalScoring: no visible global function definition for
'title'
plot.MACATevalScoring: no visible global function definition for 'axis'
plot.MACATevalScoring: no visible global function definition for
'mtext'
plot.MACATevalScoring: no visible global function definition for
'dev.off'
plotSliding: no visible global function definition for 'lines'
preprocessedLoader: no visible global function definition for
'read.delim'
preprocessedLoader: no visible global function definition for
'read.table'
preprocessedLoader: no visible global function definition for
'buildChromLocation'
preprocessedLoader: no visible global function definition for 'new'
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'
scoring : tscore: no visible global function definition for 'median'
scoring : tscoremat: no visible binding for global variable 'median'
scoring : pval: no visible binding for global variable 'pt'
scoring: no visible binding for global variable 'quantile'
Undefined global functions or variables:
addVigs2WinMenu axis browseURL buildChromLocation chromLocs
contrib.url dev.off exprs featureNames install.packages legend lines
median mtext new pData<- par png points pt quantile read.delim
read.table sampleNames title varLabels<- x11
Consider adding
importFrom("grDevices", "dev.off", "png", "x11")
importFrom("graphics", "axis", "legend", "lines", "mtext", "par",
"points", "title")
importFrom("methods", "new")
importFrom("stats", "median", "pt", "quantile")
importFrom("utils", "browseURL", "contrib.url", "install.packages",
"read.delim", "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... WARNING
prepare_Rd: man/loaddatapkg.Rd:24: unexpected '}'
* 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 include directives in Makefiles ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
discretize_tscores 13.52 0.00 13.52
get_results 6.39 0.01 6.40
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
discretize_tscores 20 0.05 20.05
get_results 8 0.02 8.02
* 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 WARNINGs, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/macat.Rcheck/00check.log'
for details.
macat.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/macat_1.58.0.tar.gz && rm -rf macat.buildbin-libdir && mkdir macat.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=macat.buildbin-libdir macat_1.58.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL macat_1.58.0.zip && rm macat_1.58.0.tar.gz macat_1.58.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 640k 100 640k 0 0 9882k 0 --:--:-- --:--:-- --:--:-- 10.7M
install for i386
* installing *source* package 'macat' ...
** using staged installation
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
Warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6rtDdB/R.INSTALL124c3f324a76/macat/man/loaddatapkg.Rd:24: unexpected '}'
*** installing help indices
converting help for package 'macat'
finding HTML links ... done
buildMACAT html
compute_sliding html
discreteKernelize html
discretize html
discretizeAll html
discretize_tscores html
evalScoring html
evaluateParameters html
get_results html
html html
kernelize html
kernelizeAll html
kernelizeToPython html
kernels html
loaddatapkg html
macat-internal html
plot_MACATevalScoring html
preprocessedLoader html
pythondata html
scoring html
stjd html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'macat' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'macat' as macat_1.58.0.zip
* DONE (macat)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'macat' successfully unpacked and MD5 sums checked
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macat.Rcheck/examples_i386/macat-Ex.timings
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macat.Rcheck/examples_x64/macat-Ex.timings
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