Luigi Marchionni
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/RTopper |
| Branch: RELEASE_3_9 |
| Last Commit: 999af30 |
| Last Changed Date: 2019-05-02 11:53:29 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:25:40 -0400 (Wed, 16 Oct 2019).
| Package 1434/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| RTopper 1.30.0 Luigi Marchionni
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: RTopper |
| Version: 1.30.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RTopper.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings RTopper_1.30.0.tar.gz |
| StartedAt: 2019-10-16 06:49:37 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 06:52:02 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 144.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: RTopper.Rcheck |
| Warnings: 1 |
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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:RTopper.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings RTopper_1.30.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/RTopper.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 'RTopper/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RTopper' version '1.30.0'
* 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 'RTopper' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpugMM8H/R.INSTALL1390438021bb/RTopper/man/fgsList.Rd:37: file link 'org.Hs.eg' in package 'org.Hs.eg.db' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpugMM8H/R.INSTALL1390438021bb/RTopper/man/fgsList.Rd:41: file link 'GO' in package 'GO.db' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpugMM8H/R.INSTALL1390438021bb/RTopper/man/fgsList.Rd:42: file link 'KEGG' in package 'KEGG.db' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/RTopper.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:
'limma'
A package should be listed in only one of these fields.
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
computeScore: no visible global function definition for 'glm'
computeScore: no visible global function definition for 'binomial'
computeScore: no visible global function definition for 'AIC'
convertToDr: no visible binding for global variable 'data'
myMean : medianM: no visible binding for global variable 'median'
Undefined global functions or variables:
AIC binomial data glm median
Consider adding
importFrom("stats", "AIC", "binomial", "glm", "median")
importFrom("utils", "data")
to your NAMESPACE file.
* 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
computeDrStat 12.41 0.17 12.59
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
computeDrStat 13.5 0.04 13.53
* 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, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/RTopper.Rcheck/00check.log'
for details.
RTopper.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/RTopper_1.30.0.tar.gz && rm -rf RTopper.buildbin-libdir && mkdir RTopper.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RTopper.buildbin-libdir RTopper_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL RTopper_1.30.0.zip && rm RTopper_1.30.0.tar.gz RTopper_1.30.0.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 1094k 100 1094k 0 0 6347k 0 --:--:-- --:--:-- --:--:-- 6631k
install for i386
* installing *source* package 'RTopper' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'RTopper'
finding HTML links ... done
RTopper-package html
adjustPvalGSE html
finding level-2 HTML links ... done
combineGSE html
computeDrStat html
convertToDr html
dat html
fgsList html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpugMM8H/R.INSTALL1390438021bb/RTopper/man/fgsList.Rd:37: file link 'org.Hs.eg' in package 'org.Hs.eg.db' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpugMM8H/R.INSTALL1390438021bb/RTopper/man/fgsList.Rd:41: file link 'GO' in package 'GO.db' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpugMM8H/R.INSTALL1390438021bb/RTopper/man/fgsList.Rd:42: file link 'KEGG' in package 'KEGG.db' does not exist and so has been treated as a topic
gseResultsSep html
intScores html
pheno html
runBatchGSE html
sepScores 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 'RTopper' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RTopper' as RTopper_1.30.0.zip
* DONE (RTopper)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'RTopper' successfully unpacked and MD5 sums checked
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RTopper.Rcheck/examples_i386/RTopper-Ex.timings
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RTopper.Rcheck/examples_x64/RTopper-Ex.timings
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