BioC 3.1: CHECK report for NormqPCR on moscato2
This page was generated on 2015-10-09 09:29:20 -0700 (Fri, 09 Oct 2015).
NormqPCR 1.14.0
James Perkins
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/NormqPCR | | Last Changed Rev: 102591 / Revision: 109384 | | Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK | |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
Summary
| Package: NormqPCR
|
| Version: 1.14.0
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| Command: rm -rf NormqPCR.buildbin-libdir NormqPCR.Rcheck && mkdir NormqPCR.buildbin-libdir NormqPCR.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=NormqPCR.buildbin-libdir NormqPCR_1.14.0.tar.gz >NormqPCR.Rcheck\00install.out 2>&1 && cp NormqPCR.Rcheck\00install.out NormqPCR-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=NormqPCR.buildbin-libdir --install="check:NormqPCR-install.out" --force-multiarch --no-vignettes --timings NormqPCR_1.14.0.tar.gz
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| StartedAt: 2015-10-09 04:26:17 -0700 (Fri, 09 Oct 2015)
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| EndedAt: 2015-10-09 04:30:24 -0700 (Fri, 09 Oct 2015)
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| EllapsedTime: 247.4 seconds
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| RetCode: 0
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| Status: OK
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| CheckDir: NormqPCR.Rcheck
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| Warnings: 0
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Command output
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### Running command:
###
### rm -rf NormqPCR.buildbin-libdir NormqPCR.Rcheck && mkdir NormqPCR.buildbin-libdir NormqPCR.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=NormqPCR.buildbin-libdir NormqPCR_1.14.0.tar.gz >NormqPCR.Rcheck\00install.out 2>&1 && cp NormqPCR.Rcheck\00install.out NormqPCR-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=NormqPCR.buildbin-libdir --install="check:NormqPCR-install.out" --force-multiarch --no-vignettes --timings NormqPCR_1.14.0.tar.gz
###
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/NormqPCR.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'NormqPCR/DESCRIPTION' ... OK
* this is package 'NormqPCR' version '1.14.0'
* 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 'NormqPCR' 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
ComputeNRQs,qPCRBatch : .local: no visible global function definition
for 'effs'
ComputeNRQs,qPCRBatch : .local: no visible global function definition
for 'se.effs'
CqValues,CyclesSet : .local: no visible binding for global variable
'l5'
CqValues,CyclesSet : .local: no visible global function definition for
'effs<-'
CqValues,CyclesSet : .local: no visible global function definition for
'se.effs<-'
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [75s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
CqValues 67.91 0.04 69.48
** running examples for arch 'x64' ... [71s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
CqValues 66.38 0.03 66.42
* 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
'E:/biocbld/bbs-3.1-bioc/meat/NormqPCR.Rcheck/00check.log'
for details.
NormqPCR.Rcheck/00install.out:
install for i386
* installing *source* package 'NormqPCR' ...
** R
** data
*** moving datasets to lazyload DB
** 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 'NormqPCR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'NormqPCR' as NormqPCR_1.14.0.zip
* DONE (NormqPCR)
NormqPCR.Rcheck/examples_i386/NormqPCR-Ex.timings:
| name | user | system | elapsed
|
| Bladder | 0.04 | 0.02 | 0.04 |
|
| BladderRepro | 0.01 | 0.00 | 0.02 |
|
| Colon | 0.02 | 0.00 | 0.01 |
|
| ComputeNRQs | 0.23 | 0.00 | 0.63 |
|
| CqValues | 67.91 | 0.04 | 69.48 |
|
| NormqPCR-package | 0 | 0 | 0 |
|
| combineTechReps | 0.06 | 0.00 | 0.06 |
|
| combineTechRepsSD | 0.06 | 0.00 | 0.08 |
|
| deltaCt | 0.12 | 0.00 | 0.13 |
|
| deltaDeltaCt | 0.14 | 0.00 | 0.14 |
|
| geNorm | 0.02 | 0.00 | 0.01 |
|
| geomMean | 0 | 0 | 0 |
|
| makeAllNAs | 0.14 | 0.00 | 0.14 |
|
| makeAllNewVal | 0.14 | 0.00 | 0.14 |
|
| replaceAboveCutOff | 0.12 | 0.00 | 0.13 |
|
| replaceNAs | 0.15 | 0.00 | 0.14 |
|
| selectHKs | 0.03 | 0.00 | 0.03 |
|
| stabMeasureM | 0.01 | 0.02 | 0.03 |
|
| stabMeasureRho | 0.03 | 0.00 | 0.03 |
|
NormqPCR.Rcheck/examples_x64/NormqPCR-Ex.timings:
| name | user | system | elapsed
|
| Bladder | 0.02 | 0.02 | 0.03 |
|
| BladderRepro | 0.02 | 0.00 | 0.01 |
|
| Colon | 0.01 | 0.00 | 0.02 |
|
| ComputeNRQs | 0.20 | 0.02 | 0.22 |
|
| CqValues | 66.38 | 0.03 | 66.42 |
|
| NormqPCR-package | 0 | 0 | 0 |
|
| combineTechReps | 0.08 | 0.00 | 0.08 |
|
| combineTechRepsSD | 0.08 | 0.00 | 0.08 |
|
| deltaCt | 0.12 | 0.00 | 0.12 |
|
| deltaDeltaCt | 0.18 | 0.00 | 0.17 |
|
| geNorm | 0.01 | 0.00 | 0.02 |
|
| geomMean | 0 | 0 | 0 |
|
| makeAllNAs | 0.17 | 0.00 | 0.17 |
|
| makeAllNewVal | 0.17 | 0.00 | 0.17 |
|
| replaceAboveCutOff | 0.13 | 0.01 | 0.14 |
|
| replaceNAs | 0.12 | 0.00 | 0.13 |
|
| selectHKs | 0.05 | 0.00 | 0.05 |
|
| stabMeasureM | 0.03 | 0.00 | 0.03 |
|
| stabMeasureRho | 0.03 | 0.00 | 0.03 |
|