| Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:07:14 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
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To the developers/maintainers of the Risa package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Risa.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1613/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Risa 1.36.0 (landing page) Alejandra Gonzalez-Beltran
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: Risa |
| Version: 1.36.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Risa.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings Risa_1.36.0.tar.gz |
| StartedAt: 2022-04-13 01:45:21 -0400 (Wed, 13 Apr 2022) |
| EndedAt: 2022-04-13 01:52:15 -0400 (Wed, 13 Apr 2022) |
| EllapsedTime: 413.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Risa.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Risa.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings Risa_1.36.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/Risa.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Risa/DESCRIPTION' ... OK
* this is package 'Risa' version '1.36.0'
* 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 'Risa' 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
* 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
getPackagesInBiocView: no visible global function definition for 'data'
readISAtabZip: no visible global function definition for 'unzip'
suggestBiocPackage: no visible global function definition for
'read.csv'
write.assay.file: no visible global function definition for
'write.table'
write.investigation.file: no visible global function definition for
'write.table'
write.study.file: no visible global function definition for
'write.table'
initialize,ISATab: no visible global function definition for
'count.fields'
initialize,ISATab: no visible global function definition for
'read.table'
initialize,ISATab : <anonymous>: no visible global function definition
for 'read.table'
initialize,ISATab : <anonymous> : <anonymous>: no visible global
function definition for 'read.table'
initialize,ISATab: no visible global function definition for 'na.omit'
Undefined global functions or variables:
count.fields data na.omit read.csv read.table unzip write.table
Consider adding
importFrom("stats", "na.omit")
importFrom("utils", "count.fields", "data", "read.csv", "read.table",
"unzip", "write.table")
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
processAssayXcmsSet.1factor 1.37 0.03 30.95
Risa-package 0.57 0.31 10.60
processAssayXcmsSet 0.81 0.00 29.44
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
processAssayXcmsSet.1factor 1.51 0.00 29.93
processAssayXcmsSet 0.94 0.02 26.41
* 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:/Users/biocbuild/bbs-3.14-bioc/meat/Risa.Rcheck/00check.log'
for details.
Risa.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/Risa_1.36.0.tar.gz && rm -rf Risa.buildbin-libdir && mkdir Risa.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Risa.buildbin-libdir Risa_1.36.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL Risa_1.36.0.zip && rm Risa_1.36.0.tar.gz Risa_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
30 2202k 30 664k 0 0 855k 0 0:00:02 --:--:-- 0:00:02 856k
100 2202k 100 2202k 0 0 1321k 0 0:00:01 0:00:01 --:--:-- 1322k
install for i386
* installing *source* package 'Risa' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'Risa'
finding HTML links ... done
AssayTab-class html
ISAtab-class html
Risa-package html
getAnnotatedDataFrameAssay html
getAssayRawDataFilenames-methods html
getExpressionSet html
getMIAMEMetadata html
getMSAssayFilenames html
getMicroarrayAssayFilenames html
getRawDataFilenames-methods html
getStudyFilename html
isMSAssay html
isMicroarrayAssay html
processAssayXcmsSet.1factor html
processAssayXcmsSet html
readISAtab html
suggestBiocPackage html
updateAssayMetadata html
write.assay.file html
write.investigation.file html
write.isatab html
write.study.file html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'Risa' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Risa' as Risa_1.36.0.zip
* DONE (Risa)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'Risa' successfully unpacked and MD5 sums checked
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Risa.Rcheck/examples_i386/Risa-Ex.timings
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Risa.Rcheck/examples_x64/Risa-Ex.timings
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