Zhicheng Ji
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/GSCA |
| git_branch: RELEASE_3_13 |
| git_last_commit: 24c5884 |
| git_last_commit_date: 2021-05-19 12:02:57 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:07 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the GSCA package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GSCA.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 817/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GSCA 2.22.0 (landing page) Zhicheng Ji
| nebbiolo1 | Linux (Ubuntu 20.04.2 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: GSCA |
| Version: 2.22.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GSCA.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings GSCA_2.22.0.tar.gz |
| StartedAt: 2021-10-15 00:08:04 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 00:14:42 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 398.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GSCA.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GSCA.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings GSCA_2.22.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/GSCA.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GSCA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GSCA' version '2.22.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'shiny', 'sp', 'gplots', 'ggplot2', 'reshape2', 'RColorBrewer',
'rhdf5'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'GSCA' 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 ... NOTE
'library' or 'require' calls in package code:
'Affyhgu133A2Expr' 'Affyhgu133Plus2Expr' 'Affyhgu133aExpr'
'Affymoe4302Expr'
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GSCA: no visible global function definition for 'data'
GSCA: no visible binding for global variable 'Affyhgu133aExprtab'
GSCA: no visible binding for global variable 'Affymoe4302Exprtab'
GSCA: no visible binding for global variable 'Affyhgu133A2Exprtab'
GSCA: no visible binding for global variable 'Affyhgu133Plus2Exprtab'
GSCA: no visible binding for global variable 'geneid'
GSCA: no visible global function definition for 'qnorm'
GSCA: no visible global function definition for 'sd'
GSCA: no visible global function definition for 'quantile'
GSCA: no visible global function definition for 'fisher.test'
GSCAeda: no visible global function definition for 'data'
GSCAeda: no visible binding for global variable 'Affyhgu133aExprtab'
GSCAeda: no visible binding for global variable 'Affymoe4302Exprtab'
GSCAeda: no visible binding for global variable 'Affyhgu133A2Exprtab'
GSCAeda: no visible binding for global variable
'Affyhgu133Plus2Exprtab'
GSCAeda: no visible binding for global variable 'geneid'
GSCAeda: no visible global function definition for 'qnorm'
GSCAeda: no visible global function definition for 'sd'
GSCAeda: no visible global function definition for 'quantile'
GSCAeda: no visible global function definition for 'pdf'
GSCAeda: no visible global function definition for 'str'
GSCAeda: no visible binding for global variable 'variable'
GSCAeda: no visible binding for global variable 'value'
GSCAeda: no visible binding for global variable 'SampleType'
GSCAeda: no visible global function definition for 'par'
GSCAeda: no visible global function definition for 'colorRampPalette'
GSCAeda: no visible global function definition for 't.test'
GSCAeda: no visible binding for global variable 'Var1'
GSCAeda: no visible binding for global variable 'Var2'
GSCAeda: no visible binding for global variable 't.stat'
GSCAeda: no visible binding for global variable 'P.value'
GSCAeda: no visible global function definition for 'fisher.test'
GSCAeda: no visible global function definition for 'dev.off'
GSCAeda: no visible global function definition for 'write.csv'
GSCAeda: no visible global function definition for 'write.table'
GSCAplot: no visible global function definition for 'data'
GSCAplot: no visible binding for global variable 'Affyhgu133aExprtab'
GSCAplot: no visible binding for global variable 'Affymoe4302Exprtab'
GSCAplot: no visible binding for global variable 'Affyhgu133A2Exprtab'
GSCAplot: no visible binding for global variable
'Affyhgu133Plus2Exprtab'
GSCAplot: no visible global function definition for 'pdf'
GSCAplot: no visible global function definition for 'par'
GSCAplot: no visible global function definition for 'hist'
GSCAplot: no visible global function definition for 'title'
GSCAplot: no visible global function definition for 'dev.off'
annotatePeaks: no visible binding for global variable 'allreffile'
tabSearch: no visible global function definition for 'data'
tabSearch: no visible binding for global variable 'Affyhgu133aExprtab'
tabSearch: no visible binding for global variable 'Affymoe4302Exprtab'
tabSearch: no visible binding for global variable 'Affyhgu133A2Exprtab'
tabSearch: no visible binding for global variable
'Affyhgu133Plus2Exprtab'
Undefined global functions or variables:
Affyhgu133A2Exprtab Affyhgu133Plus2Exprtab Affyhgu133aExprtab
Affymoe4302Exprtab P.value SampleType Var1 Var2 allreffile
colorRampPalette data dev.off fisher.test geneid hist par pdf qnorm
quantile sd str t.stat t.test title value variable write.csv
write.table
Consider adding
importFrom("grDevices", "colorRampPalette", "dev.off", "pdf")
importFrom("graphics", "hist", "par", "title")
importFrom("stats", "fisher.test", "qnorm", "quantile", "sd", "t.test")
importFrom("utils", "data", "str", "write.csv", "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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
GSCA 81.01 3.89 89.92
GSCAplot 22.14 0.94 23.10
annotatePeaks 6.14 0.64 7.68
ConstructTG 4.88 0.13 7.54
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
GSCA 87.33 4.27 101.19
GSCAplot 30.77 1.33 34.48
ConstructTG 5.54 0.08 5.86
annotatePeaks 5.36 0.15 5.89
GSCAeda 5.26 0.06 6.53
* 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: 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/GSCA.Rcheck/00check.log'
for details.
GSCA.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/GSCA_2.22.0.tar.gz && rm -rf GSCA.buildbin-libdir && mkdir GSCA.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GSCA.buildbin-libdir GSCA_2.22.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL GSCA_2.22.0.zip && rm GSCA_2.22.0.tar.gz GSCA_2.22.0.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
61 2154k 61 1318k 0 0 1312k 0 0:00:01 0:00:01 --:--:-- 1314k
100 2154k 100 2154k 0 0 1557k 0 0:00:01 0:00:01 --:--:-- 1558k
install for i386
* installing *source* package 'GSCA' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'GSCA'
finding HTML links ... done
ConstructTG html
GSCA-package html
GSCA html
GSCAeda html
GSCAplot html
GSCAui html
Oct4ESC_TG html
STAT1_TG html
annotatePeaks html
geneIDdata html
tabSearch 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 'GSCA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GSCA' as GSCA_2.22.0.zip
* DONE (GSCA)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'GSCA' successfully unpacked and MD5 sums checked
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GSCA.Rcheck/examples_i386/GSCA-Ex.timings
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GSCA.Rcheck/examples_x64/GSCA-Ex.timings
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