James Perkins
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/ReadqPCR |
| Branch: RELEASE_3_7 |
| Last Commit: 1876ef7 |
| Last Changed Date: 2018-04-30 10:35:19 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:35:29 -0400 (Wed, 17 Oct 2018).
| Package 1209/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ReadqPCR 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 | OK | OK | |
| Package: ReadqPCR |
| Version: 1.26.0 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ReadqPCR.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings ReadqPCR_1.26.0.tar.gz |
| StartedAt: 2018-10-17 04:19:20 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 04:20:20 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 60.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ReadqPCR.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ReadqPCR.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings ReadqPCR_1.26.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/ReadqPCR.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 'ReadqPCR/DESCRIPTION' ... OK
* this is package 'ReadqPCR' 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 'ReadqPCR' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpYhi8Ch/R.INSTALL16043dfc48b1/ReadqPCR/man/qpcR2CyclesSet.Rd:30: file link 'reps' in package 'qpcR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpYhi8Ch/R.INSTALL16043dfc48b1/ReadqPCR/man/read.qPCR.Rd:43: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpYhi8Ch/R.INSTALL16043dfc48b1/ReadqPCR/man/read.taqman.Rd:46: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpYhi8Ch/R.INSTALL16043dfc48b1/ReadqPCR/man/readLC480.Rd:61: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpYhi8Ch/R.INSTALL16043dfc48b1/ReadqPCR/man/readLC480SampleInfo.Rd:54: file link 'AnnotatedDataFrame-class' in package 'Biobase' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/ReadqPCR.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
'Biobase'
A package should be listed in only one of these fields.
* 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
Packages in Depends field not imported from:
'affy' 'methods'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.read.TaqBatch: no visible global function definition for 'read.delim'
.read.qPCR: no visible global function definition for 'read.table'
.readLC480txt: no visible global function definition for 'read.table'
.readLC480txt: no visible global function definition for
'AnnotatedDataFrame'
.readLC480txt: no visible global function definition for 'new'
qpcR2CyclesSet: no visible global function definition for 'new'
read.LC480SampleInfo: no visible global function definition for
'read.table'
read.LC480SampleInfo: no visible global function definition for
'AnnotatedDataFrame'
read.qPCR: no visible global function definition for 'new'
read.qPCR: no visible global function definition for 'pData'
read.qPCR: no visible global function definition for 'assayDataNew'
read.taqman: no visible global function definition for 'new'
read.taqman: no visible global function definition for 'pData'
read.taqman: no visible global function definition for 'assayDataNew'
effs,qPCRBatch: no visible global function definition for 'fData'
effs<-,qPCRBatch: no visible global function definition for 'fData'
effs<-,qPCRBatch: no visible global function definition for 'fData<-'
exprs.well.order,qPCRBatch: no visible global function definition for
'assayDataElement'
exprs.well.order<-,qPCRBatch: no visible global function definition for
'assayDataElementReplace'
exprs,CyclesSet: no visible global function definition for
'assayDataElement'
exprs,qPCRBatch: no visible global function definition for
'assayDataElement'
exprs<-,CyclesSet-ANY: no visible global function definition for
'assayDataElementReplace'
exprs<-,qPCRBatch-ANY: no visible global function definition for
'assayDataElementReplace'
merge,AnnotatedDataFrame-eSet: no visible global function definition
for 'pData'
merge,eSet-AnnotatedDataFrame: no visible global function definition
for 'pData'
merge,eSet-AnnotatedDataFrame: no visible global function definition
for 'varMetadata'
merge,eSet-AnnotatedDataFrame: no visible global function definition
for 'phenoData'
merge,eSet-AnnotatedDataFrame: no visible global function definition
for 'pData<-'
merge,eSet-AnnotatedDataFrame: no visible global function definition
for 'varMetadata<-'
merge,eSet-AnnotatedDataFrame: no visible global function definition
for 'phenoData<-'
merge,eSet-AnnotatedDataFrame: no visible global function definition
for 'featureData'
merge,eSet-AnnotatedDataFrame: no visible global function definition
for 'fData<-'
merge,eSet-AnnotatedDataFrame: no visible global function definition
for 'featureData<-'
merge,eSet-AnnotatedDataFrame: no visible global function definition
for 'protocolData'
merge,eSet-AnnotatedDataFrame: no visible global function definition
for 'protocolData<-'
se.effs,qPCRBatch: no visible global function definition for 'fData'
se.effs<-,qPCRBatch: no visible global function definition for 'fData'
se.effs<-,qPCRBatch: no visible global function definition for
'fData<-'
se.exprs,qPCRBatch: no visible global function definition for
'assayDataElement'
se.exprs<-,qPCRBatch: no visible global function definition for
'assayDataElementReplace'
Undefined global functions or variables:
AnnotatedDataFrame assayDataElement assayDataElementReplace
assayDataNew fData fData<- featureData featureData<- new pData
pData<- phenoData phenoData<- protocolData protocolData<- read.delim
read.table varMetadata varMetadata<-
Consider adding
importFrom("methods", "new")
importFrom("utils", "read.delim", "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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' ... OK
** running examples for arch 'x64' ... 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 WARNING, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.7-bioc/meat/ReadqPCR.Rcheck/00check.log'
for details.
ReadqPCR.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/ReadqPCR_1.26.0.tar.gz && rm -rf ReadqPCR.buildbin-libdir && mkdir ReadqPCR.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ReadqPCR.buildbin-libdir ReadqPCR_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL ReadqPCR_1.26.0.zip && rm ReadqPCR_1.26.0.tar.gz ReadqPCR_1.26.0.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 432k 100 432k 0 0 6710k 0 --:--:-- --:--:-- --:--:-- 7336k
install for i386
* installing *source* package 'ReadqPCR' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'ReadqPCR'
finding HTML links ... done
CyclesSet-class html
ReadqPCR-package html
merge html
qPCRBatch-class html
qpcR2CyclesSet html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpYhi8Ch/R.INSTALL16043dfc48b1/ReadqPCR/man/qpcR2CyclesSet.Rd:30: file link 'reps' in package 'qpcR' does not exist and so has been treated as a topic
read.qPCR html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpYhi8Ch/R.INSTALL16043dfc48b1/ReadqPCR/man/read.qPCR.Rd:43: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
read.taqman html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpYhi8Ch/R.INSTALL16043dfc48b1/ReadqPCR/man/read.taqman.Rd:46: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
readLC480 html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpYhi8Ch/R.INSTALL16043dfc48b1/ReadqPCR/man/readLC480.Rd:61: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
readLC480SampleInfo html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpYhi8Ch/R.INSTALL16043dfc48b1/ReadqPCR/man/readLC480SampleInfo.Rd:54: file link 'AnnotatedDataFrame-class' in package 'Biobase' does not exist and so has been treated as a topic
** building package indices
** installing vignettes
'ReadqPCR.Rnw'
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'ReadqPCR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ReadqPCR' as ReadqPCR_1.26.0.zip
* DONE (ReadqPCR)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'ReadqPCR' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
ReadqPCR.Rcheck/examples_i386/ReadqPCR-Ex.timings
|
ReadqPCR.Rcheck/examples_x64/ReadqPCR-Ex.timings
|