BioC 2.13: CHECK report for sSeq on moscato1
This page was generated on 2014-04-05 09:51:21 -0700 (Sat, 05 Apr 2014).
sSeq 1.0.0
Danni Yu
| Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/sSeq | | Last Changed Rev: 81642 / Revision: 88450 | | Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | [ OK ] | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK |
Summary
| Package: sSeq
|
| Version: 1.0.0
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| Command: rm -rf sSeq.buildbin-libdir && mkdir sSeq.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=sSeq.buildbin-libdir sSeq_1.0.0.tar.gz >sSeq-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=sSeq.buildbin-libdir --install="check:sSeq-install.out" --force-multiarch --no-vignettes --timings sSeq_1.0.0.tar.gz && mv sSeq.buildbin-libdir/* sSeq.Rcheck/ && rmdir sSeq.buildbin-libdir
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| StartedAt: 2014-04-05 06:59:06 -0700 (Sat, 05 Apr 2014)
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| EndedAt: 2014-04-05 07:15:32 -0700 (Sat, 05 Apr 2014)
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| EllapsedTime: 986.3 seconds
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| RetCode: 0
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| Status: OK
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| CheckDir: sSeq.Rcheck
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| Warnings: 0
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Command output
* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/sSeq.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'sSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sSeq' version '1.0.0'
* 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 'sSeq' 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
* 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 'caTools' which was already attached by Depends.
Please remove these calls from your code.
Packages in Depends field not imported from:
'RColorBrewer' 'caTools'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* 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 installed files from 'inst/doc' ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
'sSeq.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [496s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
nbTestSH 164.41 0.53 164.96
getTgroup 158.65 0.90 159.56
sSeq-package 156.53 0.50 157.03
plotDispersion 5.19 0.02 5.22
** running examples for arch 'x64' ... [454s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
nbTestSH 147.34 0.50 148.16
sSeq-package 146.34 0.40 146.81
getTgroup 140.62 0.91 141.59
plotDispersion 6.63 0.00 6.63
* 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
NOTE: There were 2 notes.
See
'D:/biocbld/bbs-2.13-bioc/meat/sSeq.Rcheck/00check.log'
for details.
sSeq.Rcheck/00install.out:
install for i386
* installing *source* package 'sSeq' ...
** 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 'sSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'sSeq' as sSeq_1.0.0.zip
* DONE (sSeq)
sSeq.Rcheck/examples_i386/sSeq-Ex.timings:
| name | user | system | elapsed
|
| Hammer2months | 0.07 | 0.00 | 0.08 |
|
| Sultan | 0.08 | 0.00 | 0.07 |
|
| Tuch | 0.07 | 0.00 | 0.06 |
|
| countsTable | 0.03 | 0.00 | 0.03 |
|
| drawMA_vol | 0.36 | 0.00 | 0.36 |
|
| ecdfAUC | 0.01 | 0.00 | 0.02 |
|
| equalSpace | 0.38 | 0.00 | 0.37 |
|
| exactNBtest1 | 0 | 0 | 0 |
|
| getAdjustDisp | 0.36 | 0.00 | 0.36 |
|
| getNormFactor | 0.03 | 0.00 | 0.03 |
|
| getQ | 2.65 | 0.00 | 2.66 |
|
| getT | 3.54 | 0.00 | 3.54 |
|
| getTgroup | 158.65 | 0.90 | 159.56 |
|
| nbTestSH | 164.41 | 0.53 | 164.96 |
|
| plotDispersion | 5.19 | 0.02 | 5.22 |
|
| rnbinomMV | 0 | 0 | 0 |
|
| rowVars | 0.02 | 0.00 | 0.02 |
|
| sSeq-package | 156.53 | 0.50 | 157.03 |
|
| sim | 0.7 | 0.0 | 0.7 |
|
sSeq.Rcheck/examples_x64/sSeq-Ex.timings:
| name | user | system | elapsed
|
| Hammer2months | 0.09 | 0.01 | 0.11 |
|
| Sultan | 0.16 | 0.00 | 0.16 |
|
| Tuch | 0.09 | 0.00 | 0.09 |
|
| countsTable | 0.03 | 0.00 | 0.03 |
|
| drawMA_vol | 0.39 | 0.02 | 0.41 |
|
| ecdfAUC | 0.03 | 0.00 | 0.93 |
|
| equalSpace | 0.48 | 0.01 | 0.50 |
|
| exactNBtest1 | 0.02 | 0.00 | 0.02 |
|
| getAdjustDisp | 0.44 | 0.00 | 0.43 |
|
| getNormFactor | 0.03 | 0.00 | 0.04 |
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| getQ | 3.09 | 0.02 | 3.10 |
|
| getT | 2.95 | 0.01 | 2.96 |
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| getTgroup | 140.62 | 0.91 | 141.59 |
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| nbTestSH | 147.34 | 0.50 | 148.16 |
|
| plotDispersion | 6.63 | 0.00 | 6.63 |
|
| rnbinomMV | 0.02 | 0.00 | 0.01 |
|
| rowVars | 0 | 0 | 0 |
|
| sSeq-package | 146.34 | 0.40 | 146.81 |
|
| sim | 0.71 | 0.00 | 0.71 |
|