BioC 3.3: CHECK report for sRAP on windows2.bioconductor.org
This page was generated on 2015-10-27 12:15:26 -0400 (Tue, 27 Oct 2015).
sRAP 1.11.0 Charles Warden
Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sRAP | 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 | WARNINGS | |  |
windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ WARNINGS ] | OK |  |
Summary
Package: sRAP
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Version: 1.11.0
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Command: rm -rf sRAP.buildbin-libdir sRAP.Rcheck && mkdir sRAP.buildbin-libdir sRAP.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=sRAP.buildbin-libdir sRAP_1.11.0.tar.gz >sRAP.Rcheck\00install.out 2>&1 && cp sRAP.Rcheck\00install.out sRAP-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=sRAP.buildbin-libdir --install="check:sRAP-install.out" --force-multiarch --no-vignettes --timings sRAP_1.11.0.tar.gz
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StartedAt: 2015-10-27 06:19:15 -0400 (Tue, 27 Oct 2015)
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EndedAt: 2015-10-27 06:23:22 -0400 (Tue, 27 Oct 2015)
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EllapsedTime: 247.3 seconds
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RetCode: 0
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Status: WARNINGS
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CheckDir: sRAP.Rcheck
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Warnings: 1
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Command output
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### Running command:
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### rm -rf sRAP.buildbin-libdir sRAP.Rcheck && mkdir sRAP.buildbin-libdir sRAP.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=sRAP.buildbin-libdir sRAP_1.11.0.tar.gz >sRAP.Rcheck\00install.out 2>&1 && cp sRAP.Rcheck\00install.out sRAP-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=sRAP.buildbin-libdir --install="check:sRAP-install.out" --force-multiarch --no-vignettes --timings sRAP_1.11.0.tar.gz
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/sRAP.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 'sRAP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sRAP' version '1.11.0'
* 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 'sRAP' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
RNA.bdfunc.fc: no visible binding for global variable
'bdfunc.enrichment.human'
RNA.bdfunc.fc: no visible binding for global variable
'bdfunc.enrichment.mouse'
RNA.bdfunc.signal: no visible binding for global variable
'bdfunc.enrichment.human'
RNA.bdfunc.signal: no visible binding for global variable
'bdfunc.enrichment.mouse'
Undefined global functions or variables:
bdfunc.enrichment.human bdfunc.enrichment.mouse
* 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 ... WARNING
Note: significantly better compression could be obtained
by using R CMD build --resave-data
old_size new_size compress
bdfunc.enrichment.human.rda 1.3Mb 951Kb bzip2
bdfunc.enrichment.mouse.rda 31Kb 26Kb xz
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... NOTE
The following files look like leftovers/mistakes:
'sRAP.bbl'
Please remove them from your package.
* checking examples ...
** running examples for arch 'i386' ... [96s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
RNA.bdfunc.signal 56.00 0.05 60.61
RNA.bdfunc.fc 9.17 0.02 14.75
RNA.deg 8.48 0.01 13.33
** running examples for arch 'x64' ... [118s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
RNA.bdfunc.signal 75.48 0.04 80.09
RNA.bdfunc.fc 10.82 0.00 15.25
RNA.deg 9.16 0.02 13.66
* 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:/biocbld/bbs-3.3-bioc/meat/sRAP.Rcheck/00check.log'
for details.
sRAP.Rcheck/00install.out:
install for i386
* installing *source* package 'sRAP' ...
** R
** data
** 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 'sRAP' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'sRAP' as sRAP_1.11.0.zip
* DONE (sRAP)
sRAP.Rcheck/examples_i386/sRAP-Ex.timings:
name | user | system | elapsed
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RNA.bdfunc.fc | 9.17 | 0.02 | 14.75 |
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RNA.bdfunc.signal | 56.00 | 0.05 | 60.61 |
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RNA.deg | 8.48 | 0.01 | 13.33 |
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RNA.norm | 1.85 | 0.00 | 3.34 |
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RNA.prepare.input | 0.00 | 0.00 | 0.24 |
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RNA.qc | 1.86 | 0.02 | 3.36 |
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sRAP.Rcheck/examples_x64/sRAP-Ex.timings:
name | user | system | elapsed
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RNA.bdfunc.fc | 10.82 | 0.00 | 15.25 |
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RNA.bdfunc.signal | 75.48 | 0.04 | 80.09 |
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RNA.deg | 9.16 | 0.02 | 13.66 |
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RNA.norm | 1.65 | 0.00 | 3.92 |
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RNA.prepare.input | 0.02 | 0.00 | 0.24 |
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RNA.qc | 1.64 | 0.00 | 3.73 |
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