Valentin Dinu
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/PoTRA |
| Branch: master |
| Last Commit: aa5b254 |
| Last Changed Date: 2019-04-08 16:42:41 -0400 (Mon, 08 Apr 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 12:45:11 -0400 (Tue, 09 Apr 2019).
| Package 1209/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| PoTRA 0.99.83 Valentin Dinu
| 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 | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK |
| Package: PoTRA |
| Version: 0.99.83 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PoTRA.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings PoTRA_0.99.83.tar.gz |
| StartedAt: 2019-04-09 05:00:16 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 05:01:56 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 99.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: PoTRA.Rcheck |
| Warnings: 4 |
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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:PoTRA.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings PoTRA_0.99.83.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/PoTRA.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PoTRA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PoTRA' version '0.99.83'
* package encoding: UTF-8
* checking package namespace information ... NOTE
Namespaces with empty importFrom:
'BiocGenerics' 'graph' 'org.Hs.eg.db'
* 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 'PoTRA' can be installed ... WARNING
Found the following significant warnings:
Warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiCDGnZ/R.INSTALLc343b3d6bf8/PoTRA/man/man.Rd:12: unexpected UNKNOWN '\arguements'
Warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiCDGnZ/R.INSTALLc343b3d6bf8/PoTRA/man/man.Rd:25: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiCDGnZ/R.INSTALLc343b3d6bf8/PoTRA/man/man.Rd:26: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiCDGnZ/R.INSTALLc343b3d6bf8/PoTRA/man/man.Rd:27: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiCDGnZ/R.INSTALLc343b3d6bf8/PoTRA/man/man.Rd:28: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiCDGnZ/R.INSTALLc343b3d6bf8/PoTRA/man/man.Rd:13: All text must be in a section
Warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiCDGnZ/R.INSTALLc343b3d6bf8/PoTRA/man/man.Rd:14: All text must be in a section
Warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiCDGnZ/R.INSTALLc343b3d6bf8/PoTRA/man/man.Rd:15: All text must be in a section
Warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiCDGnZ/R.INSTALLc343b3d6bf8/PoTRA/man/man.Rd:16: All text must be in a section
Warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiCDGnZ/R.INSTALLc343b3d6bf8/PoTRA/man/man.Rd:17: All text must be in a section
Warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiCDGnZ/R.INSTALLc343b3d6bf8/PoTRA/man/man.Rd:18: All text must be in a section
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/PoTRA.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 ... OK
* 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 ... WARNING
prepare_Rd: man/man.Rd:12: unexpected UNKNOWN '\arguements'
prepare_Rd: man/man.Rd:25: unknown macro '\item'
prepare_Rd: man/man.Rd:26: unknown macro '\item'
prepare_Rd: man/man.Rd:27: unknown macro '\item'
prepare_Rd: man/man.Rd:28: unknown macro '\item'
prepare_Rd: man.Rd:13: All text must be in a section
prepare_Rd: man.Rd:14: All text must be in a section
prepare_Rd: man.Rd:15: All text must be in a section
prepare_Rd: man.Rd:16: All text must be in a section
prepare_Rd: man.Rd:17: All text must be in a section
prepare_Rd: man.Rd:18: All text must be in a section
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
'PoTRA.corN'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Assignments in \usage in documentation object 'PoTRA':
Results <- PoTRA.corN(mydata = mydata, genelist = genelist, Num.sample.normal = Num.sample.normal,
Num.sample.case = Num.sample.case, Pathway.database = Pathway.database,
PR.quantile = PR.quantile)
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ... NONE
* 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: 4 WARNINGs, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/PoTRA.Rcheck/00check.log'
for details.
PoTRA.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/PoTRA_0.99.83.tar.gz && rm -rf PoTRA.buildbin-libdir && mkdir PoTRA.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PoTRA.buildbin-libdir PoTRA_0.99.83.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL PoTRA_0.99.83.zip && rm PoTRA_0.99.83.tar.gz PoTRA_0.99.83.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 10308 100 10308 0 0 168k 0 --:--:-- --:--:-- --:--:-- 189k
install for i386
* installing *source* package 'PoTRA' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
Warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiCDGnZ/R.INSTALLc343b3d6bf8/PoTRA/man/man.Rd:12: unexpected UNKNOWN '\arguements'
Warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiCDGnZ/R.INSTALLc343b3d6bf8/PoTRA/man/man.Rd:25: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiCDGnZ/R.INSTALLc343b3d6bf8/PoTRA/man/man.Rd:26: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiCDGnZ/R.INSTALLc343b3d6bf8/PoTRA/man/man.Rd:27: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiCDGnZ/R.INSTALLc343b3d6bf8/PoTRA/man/man.Rd:28: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiCDGnZ/R.INSTALLc343b3d6bf8/PoTRA/man/man.Rd:13: All text must be in a section
Warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiCDGnZ/R.INSTALLc343b3d6bf8/PoTRA/man/man.Rd:13: All text must be in a section
Warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiCDGnZ/R.INSTALLc343b3d6bf8/PoTRA/man/man.Rd:14: All text must be in a section
Warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiCDGnZ/R.INSTALLc343b3d6bf8/PoTRA/man/man.Rd:14: All text must be in a section
Warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiCDGnZ/R.INSTALLc343b3d6bf8/PoTRA/man/man.Rd:15: All text must be in a section
Warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiCDGnZ/R.INSTALLc343b3d6bf8/PoTRA/man/man.Rd:15: All text must be in a section
Warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiCDGnZ/R.INSTALLc343b3d6bf8/PoTRA/man/man.Rd:16: All text must be in a section
Warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiCDGnZ/R.INSTALLc343b3d6bf8/PoTRA/man/man.Rd:16: All text must be in a section
Warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiCDGnZ/R.INSTALLc343b3d6bf8/PoTRA/man/man.Rd:17: All text must be in a section
Warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiCDGnZ/R.INSTALLc343b3d6bf8/PoTRA/man/man.Rd:17: All text must be in a section
Warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiCDGnZ/R.INSTALLc343b3d6bf8/PoTRA/man/man.Rd:18: All text must be in a section
Warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiCDGnZ/R.INSTALLc343b3d6bf8/PoTRA/man/man.Rd:18: All text must be in a section
*** installing help indices
converting help for package 'PoTRA'
finding HTML links ... done
man 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 'PoTRA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PoTRA' as PoTRA_0.99.83.zip
* DONE (PoTRA)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'PoTRA' successfully unpacked and MD5 sums checked