James Perkins
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/NormqPCR |
| Branch: RELEASE_3_7 |
| Last Commit: 43ca4a8 |
| Last Changed Date: 2018-04-30 10:35:20 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:35:33 -0400 (Wed, 17 Oct 2018).
| Package 1000/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| NormqPCR 1.26.0 James Perkins
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: NormqPCR |
| Version: 1.26.0 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:NormqPCR.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings NormqPCR_1.26.0.tar.gz |
| StartedAt: 2018-10-17 03:40:47 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 03:44:21 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 214.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: NormqPCR.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:NormqPCR.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings NormqPCR_1.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/NormqPCR.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.26.0'
* 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 ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0oA3mk/R.INSTALL11487b95f2e/NormqPCR/man/ComputeNRQs.Rd:14: file link 'qPCRBatch' in package 'ReadqPCR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0oA3mk/R.INSTALL11487b95f2e/NormqPCR/man/CqValues.Rd:23: file link 'CyclesSet' in package 'ReadqPCR' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/NormqPCR.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 ... NOTE
stabMeasureM: no visible global function definition for 'sd'
ComputeNRQs,qPCRBatch: no visible global function definition for 'effs'
ComputeNRQs,qPCRBatch: no visible global function definition for
'se.effs'
CqValues,CyclesSet: no visible binding for global variable 'l5'
CqValues,CyclesSet: no visible global function definition for 'effs<-'
CqValues,CyclesSet: no visible global function definition for
'se.effs<-'
combineTechReps,qPCRBatch: no visible binding for global variable
'median'
combineTechRepsWithSD,qPCRBatch: no visible binding for global variable
'sd'
combineTechRepsWithSD,qPCRBatch: no visible binding for global variable
'median'
combineTechRepsWithSD,qPCRBatch: no visible binding for global variable
'mad'
deltaDeltaCt,qPCRBatch: no visible global function definition for 'sd'
selectHKs,matrix: no visible global function definition for 'sd'
stabMeasureRho,matrix: no visible global function definition for
'aggregate'
Undefined global functions or variables:
aggregate effs effs<- l5 mad median sd se.effs se.effs<-
Consider adding
importFrom("stats", "aggregate", "mad", "median", "sd")
to your NAMESPACE file.
* 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' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
CqValues 47.74 0.15 48.28
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
CqValues 58.83 0.08 58.92
* 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, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.7-bioc/meat/NormqPCR.Rcheck/00check.log'
for details.
NormqPCR.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/NormqPCR_1.26.0.tar.gz && rm -rf NormqPCR.buildbin-libdir && mkdir NormqPCR.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=NormqPCR.buildbin-libdir NormqPCR_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL NormqPCR_1.26.0.zip && rm NormqPCR_1.26.0.tar.gz NormqPCR_1.26.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
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0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 313k 100 313k 0 0 4984k 0 --:--:-- --:--:-- --:--:-- 5604k
install for i386
* installing *source* package 'NormqPCR' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'NormqPCR'
finding HTML links ... done
Bladder html
BladderRepro html
Colon html
ComputeNRQs html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0oA3mk/R.INSTALL11487b95f2e/NormqPCR/man/ComputeNRQs.Rd:14: file link 'qPCRBatch' in package 'ReadqPCR' does not exist and so has been treated as a topic
CqValues html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0oA3mk/R.INSTALL11487b95f2e/NormqPCR/man/CqValues.Rd:23: file link 'CyclesSet' in package 'ReadqPCR' does not exist and so has been treated as a topic
NormqPCR-package html
combineTechReps html
combineTechRepsSD html
deltaCt html
deltaDeltaCt html
geNorm html
geomMean html
makeAllNAs html
makeAllNewVal html
replaceAboveCutOff html
replaceNAs html
selectHKs html
stabMeasureM html
stabMeasureRho html
** building package indices
** installing vignettes
'NormqPCR.Rnw'
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'NormqPCR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'NormqPCR' as NormqPCR_1.26.0.zip
* DONE (NormqPCR)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'NormqPCR' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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NormqPCR.Rcheck/examples_i386/NormqPCR-Ex.timings
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NormqPCR.Rcheck/examples_x64/NormqPCR-Ex.timings
|