BioC 3.2: CHECK report for TEQC on windows1.bioconductor.org
This page was generated on 2015-10-27 17:29:20 -0400 (Tue, 27 Oct 2015).
TEQC 3.10.0
Manuela Hummel
| Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/TEQC | | Last Changed Rev: 109589 / Revision: 109947 | | Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015) |
| linux1.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| windows1.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
Summary
| Package: TEQC
|
| Version: 3.10.0
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| Command: rm -rf TEQC.buildbin-libdir TEQC.Rcheck && mkdir TEQC.buildbin-libdir TEQC.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=TEQC.buildbin-libdir TEQC_3.10.0.tar.gz >TEQC.Rcheck\00install.out 2>&1 && cp TEQC.Rcheck\00install.out TEQC-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=TEQC.buildbin-libdir --install="check:TEQC-install.out" --force-multiarch --no-vignettes --timings TEQC_3.10.0.tar.gz
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| StartedAt: 2015-10-27 06:05:44 -0400 (Tue, 27 Oct 2015)
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| EndedAt: 2015-10-27 06:08:38 -0400 (Tue, 27 Oct 2015)
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| EllapsedTime: 174.0 seconds
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| RetCode: 0
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| Status: OK
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| CheckDir: TEQC.Rcheck
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| Warnings: 0
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Command output
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###
### Running command:
###
### rm -rf TEQC.buildbin-libdir TEQC.Rcheck && mkdir TEQC.buildbin-libdir TEQC.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=TEQC.buildbin-libdir TEQC_3.10.0.tar.gz >TEQC.Rcheck\00install.out 2>&1 && cp TEQC.Rcheck\00install.out TEQC-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=TEQC.buildbin-libdir --install="check:TEQC-install.out" --force-multiarch --no-vignettes --timings TEQC_3.10.0.tar.gz
###
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* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/TEQC.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TEQC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TEQC' version '3.10.0'
* 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 'TEQC' 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
coverage.plot: no visible global function definition for 'Rle'
coverage.target: no visible global function definition for 'Rle'
get.reads: no visible binding for global variable 'pos'
get.reads: no visible binding for global variable 'qwidth'
get.reads: no visible binding for global variable 'qname'
get.reads: no visible binding for global variable 'rname'
multfun: no visible global function definition for 'Rle'
multfun: no visible global function definition for 'runValue'
reads2pairs: no visible global function definition for 'Rle'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [24s] OK
** running examples for arch 'x64' ... [25s] OK
* 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 NOTE
See
'C:/biocbld/bbs-3.2-bioc/meat/TEQC.Rcheck/00check.log'
for details.
TEQC.Rcheck/00install.out:
install for i386
* installing *source* package 'TEQC' ...
** R
** 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 'TEQC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TEQC' as TEQC_3.10.0.zip
* DONE (TEQC)
TEQC.Rcheck/examples_i386/TEQC-Ex.timings:
| name | user | system | elapsed
|
| TEQCreport | 0 | 0 | 0 |
|
| chrom.barplot | 0.31 | 0.00 | 0.31 |
|
| coverage.GC | 1.08 | 0.00 | 1.08 |
|
| coverage.correlation | 1.59 | 0.00 | 1.60 |
|
| coverage.density | 0.92 | 0.00 | 0.92 |
|
| coverage.hist | 1 | 0 | 1 |
|
| coverage.plot | 0.75 | 0.01 | 0.76 |
|
| coverage.target | 0.85 | 0.00 | 0.85 |
|
| coverage.targetlength.plot | 0.84 | 0.00 | 0.84 |
|
| coverage.uniformity | 0.68 | 0.00 | 0.68 |
|
| covered.k | 0.83 | 0.00 | 0.83 |
|
| duplicates.barplot | 4.6 | 0.0 | 4.6 |
|
| fraction.reads.target | 0.64 | 0.00 | 0.64 |
|
| fraction.target | 0.18 | 0.00 | 0.18 |
|
| get.baits | 0.03 | 0.00 | 0.04 |
|
| get.reads | 0.22 | 0.00 | 0.21 |
|
| get.targets | 0.16 | 0.00 | 0.16 |
|
| insert.size.hist | 1.76 | 0.02 | 1.78 |
|
| make.wigfiles | 1.03 | 0.01 | 1.04 |
|
| multiTEQCreport | 0.5 | 0.0 | 0.5 |
|
| reads2pairs | 1.56 | 0.00 | 1.56 |
|
| readsPerTarget | 0.66 | 0.02 | 0.67 |
|
TEQC.Rcheck/examples_x64/TEQC-Ex.timings:
| name | user | system | elapsed
|
| TEQCreport | 0 | 0 | 0 |
|
| chrom.barplot | 0.33 | 0.00 | 0.33 |
|
| coverage.GC | 1.19 | 0.00 | 1.19 |
|
| coverage.correlation | 1.75 | 0.00 | 1.75 |
|
| coverage.density | 1 | 0 | 1 |
|
| coverage.hist | 0.88 | 0.00 | 0.87 |
|
| coverage.plot | 0.78 | 0.00 | 0.78 |
|
| coverage.target | 0.75 | 0.00 | 0.75 |
|
| coverage.targetlength.plot | 1.07 | 0.00 | 1.08 |
|
| coverage.uniformity | 0.91 | 0.00 | 0.91 |
|
| covered.k | 0.86 | 0.00 | 0.86 |
|
| duplicates.barplot | 4.36 | 0.00 | 4.35 |
|
| fraction.reads.target | 0.41 | 0.00 | 0.41 |
|
| fraction.target | 0.14 | 0.00 | 0.14 |
|
| get.baits | 0.01 | 0.00 | 0.02 |
|
| get.reads | 0.13 | 0.00 | 0.12 |
|
| get.targets | 0.14 | 0.00 | 0.14 |
|
| insert.size.hist | 1.58 | 0.00 | 1.58 |
|
| make.wigfiles | 0.88 | 0.00 | 0.87 |
|
| multiTEQCreport | 0.32 | 0.00 | 0.33 |
|
| reads2pairs | 2.02 | 0.00 | 2.02 |
|
| readsPerTarget | 0.52 | 0.00 | 0.51 |
|