Gwenael G.R. Leday to
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/plrs |
| Branch: RELEASE_3_8 |
| Last Commit: 8a760ff |
| Last Changed Date: 2018-10-30 11:41:50 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:22:29 -0400 (Sat, 13 Apr 2019).
| Package 1170/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| plrs 1.22.0 Gwenael G.R. Leday to
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: plrs |
| Version: 1.22.0 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:plrs.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings plrs_1.22.0.tar.gz |
| StartedAt: 2019-04-13 04:35:53 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 04:38:18 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 144.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: plrs.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:plrs.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings plrs_1.22.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/plrs.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'plrs/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'plrs' version '1.22.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 'plrs' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOAgG6h/R.INSTALL1ccc21dc73ad/plrs/man/neveCN17.Rd:15: file link 'cghCall' in package 'CGHbase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOAgG6h/R.INSTALL1ccc21dc73ad/plrs/man/neveGE17.Rd:15: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOAgG6h/R.INSTALL1ccc21dc73ad/plrs/man/plrs.series.Rd:32: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOAgG6h/R.INSTALL1ccc21dc73ad/plrs/man/plrs.series.Rd:33: file link 'cghSeg' in package 'CGHbase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOAgG6h/R.INSTALL1ccc21dc73ad/plrs/man/plrs.series.Rd:33: file link 'cghCall' in package 'CGHbase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOAgG6h/R.INSTALL1ccc21dc73ad/plrs/man/plrs.series.Rd:47: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOAgG6h/R.INSTALL1ccc21dc73ad/plrs/man/plrs.series.Rd:48: file link 'cghSeg' in package 'CGHbase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOAgG6h/R.INSTALL1ccc21dc73ad/plrs/man/plrs.series.Rd:48: file link 'cghCall' in package 'CGHbase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOAgG6h/R.INSTALL1ccc21dc73ad/plrs/man/plrs.series.Rd:50: file link 'cghSeg' in package 'CGHbase' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/plrs.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
'methods'
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' call to 'mvtnorm' in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
':::' call which should be '::': 'CGHbase:::calls'
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 ... 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plrs.series 6.99 0.03 7.01
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plrs.series 6.8 0.03 6.83
* 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: 1 WARNING, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.8-bioc/meat/plrs.Rcheck/00check.log'
for details.
plrs.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/plrs_1.22.0.tar.gz && rm -rf plrs.buildbin-libdir && mkdir plrs.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=plrs.buildbin-libdir plrs_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL plrs_1.22.0.zip && rm plrs_1.22.0.tar.gz plrs_1.22.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
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install for i386
* installing *source* package 'plrs' ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'plrs'
finding HTML links ... done
criteria html
modify.conf html
neveCN17 html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOAgG6h/R.INSTALL1ccc21dc73ad/plrs/man/neveCN17.Rd:15: file link 'cghCall' in package 'CGHbase' does not exist and so has been treated as a topic
neveGE17 html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOAgG6h/R.INSTALL1ccc21dc73ad/plrs/man/neveGE17.Rd:15: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
plot-methods html
plrs-class html
plrs-package html
plrs html
plrs.cb html
plrs.select-class html
plrs.select html
plrs.series-class html
plrs.series html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOAgG6h/R.INSTALL1ccc21dc73ad/plrs/man/plrs.series.Rd:32: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOAgG6h/R.INSTALL1ccc21dc73ad/plrs/man/plrs.series.Rd:33: file link 'cghSeg' in package 'CGHbase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOAgG6h/R.INSTALL1ccc21dc73ad/plrs/man/plrs.series.Rd:33: file link 'cghCall' in package 'CGHbase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOAgG6h/R.INSTALL1ccc21dc73ad/plrs/man/plrs.series.Rd:47: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOAgG6h/R.INSTALL1ccc21dc73ad/plrs/man/plrs.series.Rd:48: file link 'cghSeg' in package 'CGHbase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOAgG6h/R.INSTALL1ccc21dc73ad/plrs/man/plrs.series.Rd:48: file link 'cghCall' in package 'CGHbase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOAgG6h/R.INSTALL1ccc21dc73ad/plrs/man/plrs.series.Rd:50: file link 'cghSeg' in package 'CGHbase' does not exist and so has been treated as a topic
plrs.sim html
plrs.test html
predict.plrs html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'plrs' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'plrs' as plrs_1.22.0.zip
* DONE (plrs)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'plrs' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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plrs.Rcheck/examples_i386/plrs-Ex.timings
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plrs.Rcheck/examples_x64/plrs-Ex.timings
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