Jonathon Blake
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/MiChip |
| Branch: RELEASE_3_8 |
| Last Commit: bec77ef |
| Last Changed Date: 2018-10-30 11:41:45 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:21:03 -0400 (Sat, 13 Apr 2019).
| Package 953/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MiChip 1.36.0 Jonathon Blake
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: MiChip |
| Version: 1.36.0 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MiChip.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings MiChip_1.36.0.tar.gz |
| StartedAt: 2019-04-13 03:49:10 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 03:50:48 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 98.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MiChip.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MiChip.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings MiChip_1.36.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/MiChip.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MiChip/DESCRIPTION' ... OK
* this is package 'MiChip' version '1.36.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 'MiChip' can be installed ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
boxplotData: no visible global function definition for 'jpeg'
boxplotData: no visible global function definition for 'boxplot'
boxplotData: no visible global function definition for 'rainbow'
boxplotData: no visible global function definition for 'dev.off'
boxplotDataNoFile: no visible global function definition for 'boxplot'
boxplotDataNoFile: no visible global function definition for 'rainbow'
correctForFlags: no visible global function definition for 'new'
myForgivingMedian: no visible global function definition for 'na.omit'
myForgivingMedian: no visible global function definition for 'median'
myForgivingMedian: no visible global function definition for 'sd'
naOmitMedian: no visible global function definition for 'na.omit'
naOmitMedian: no visible global function definition for 'mad'
naOmitMedian: no visible global function definition for 'median'
normalizePerChipMedian: no visible global function definition for
'na.omit'
normalizePerChipMedian: no visible global function definition for
'median'
normalizePerChipMedian: no visible global function definition for 'new'
outputAnnotatedDataMatrix: no visible global function definition for
'write.table'
panelCor: no visible global function definition for 'cor.test'
panelCor: no visible binding for global variable 'na.omit'
panelCor: no visible global function definition for 'strwidth'
panelCor: no visible global function definition for 'text'
parseRawData: no visible global function definition for 'read.table'
parseRawData: no visible global function definition for 'new'
plotIntensitiesScatter: no visible global function definition for
'jpeg'
plotIntensitiesScatter: no visible global function definition for
'pairs'
plotIntensitiesScatter : <anonymous>: no visible global function
definition for 'points'
plotIntensitiesScatter : <anonymous>: no visible global function
definition for 'abline'
plotIntensitiesScatter: no visible global function definition for
'dev.off'
removeUnwantedRows: no visible global function definition for 'new'
summarizeIntensitiesAsMedian: no visible binding for global variable
'median'
summarizeIntensitiesAsMedian: no visible global function definition for
'new'
Undefined global functions or variables:
abline boxplot cor.test dev.off jpeg mad median na.omit new pairs
points rainbow read.table sd strwidth text write.table
Consider adding
importFrom("grDevices", "dev.off", "jpeg", "rainbow")
importFrom("graphics", "abline", "boxplot", "pairs", "points",
"strwidth", "text")
importFrom("methods", "new")
importFrom("stats", "cor.test", "mad", "median", "na.omit", "sd")
importFrom("utils", "read.table", "write.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 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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.8-bioc/meat/MiChip.Rcheck/00check.log'
for details.
MiChip.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/MiChip_1.36.0.tar.gz && rm -rf MiChip.buildbin-libdir && mkdir MiChip.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MiChip.buildbin-libdir MiChip_1.36.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL MiChip_1.36.0.zip && rm MiChip_1.36.0.tar.gz MiChip_1.36.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 421k 100 421k 0 0 8973k 0 --:--:-- --:--:-- --:--:-- 9793k
install for i386
* installing *source* package 'MiChip' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'MiChip'
finding HTML links ... done
MiChip html
boxplotData html
boxplotDataNoFile html
correctForFlags html
myForgivingMedian html
naOmitMedian html
normalizePerChipMedian html
outputAnnotatedDataMatrix html
panelCor html
parseRawData html
plotIntensitiesScatter html
removeUnwantedRows html
returnAnnotatedDataMatrix html
setIntensityCutoff html
standardRemoveRows html
summarizeIntensitiesAsMedian html
workedExampleMedianNormalize html
workedExampleNotNormalizedData html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'MiChip' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MiChip' as MiChip_1.36.0.zip
* DONE (MiChip)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'MiChip' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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MiChip.Rcheck/examples_i386/MiChip-Ex.timings
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MiChip.Rcheck/examples_x64/MiChip-Ex.timings
|