Maren Sitte
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/pwOmics |
| git_branch: RELEASE_3_14 |
| git_last_commit: b5d245a |
| git_last_commit_date: 2021-10-26 12:20:38 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:07:08 -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 | ||||
|
To the developers/maintainers of the pwOmics package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/pwOmics.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 1492/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| pwOmics 1.26.0 (landing page) Maren Sitte
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: pwOmics |
| Version: 1.26.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pwOmics.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings pwOmics_1.26.0.tar.gz |
| StartedAt: 2022-04-13 01:02:11 -0400 (Wed, 13 Apr 2022) |
| EndedAt: 2022-04-13 01:11:05 -0400 (Wed, 13 Apr 2022) |
| EllapsedTime: 533.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: pwOmics.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pwOmics.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings pwOmics_1.26.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/pwOmics.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 'pwOmics/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pwOmics' 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 'pwOmics' can be installed ... OK
* checking installed package size ... OK
* checking package 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
identifyPWTFTGs: no visible binding for global variable 'upreg'
identifyPWTFTGs: no visible binding for global variable 'phosphoeffect'
infoConsensusGraph: no visible global function definition for 'from'
Undefined global functions or variables:
from phosphoeffect upreg
* 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 ... WARNING
Documented arguments not in \usage in documentation object 'plotTimeProfileClusters':
'...'
Documented arguments not in \usage in documentation object 'temp_correlations':
'...'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
temp_correlations 152.68 1.08 156.39
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
temp_correlations 171.28 0.79 173.74
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
Running 'runTests.R'
OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.14-bioc/meat/pwOmics.Rcheck/00check.log'
for details.
pwOmics.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/pwOmics_1.26.0.tar.gz && rm -rf pwOmics.buildbin-libdir && mkdir pwOmics.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pwOmics.buildbin-libdir pwOmics_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL pwOmics_1.26.0.zip && rm pwOmics_1.26.0.tar.gz pwOmics_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
20 892k 20 187k 0 0 498k 0 0:00:01 --:--:-- 0:00:01 498k
100 892k 100 892k 0 0 855k 0 0:00:01 0:00:01 --:--:-- 855k
install for i386
* installing *source* package 'pwOmics' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'pwOmics'
finding HTML links ... done
OmicsExampleData html
PWidentallprots html
PWidentallprotssub html
PWidenttps html
SteinerTree_cons html
TFidentallgenes html
TFidenttps html
addFeedbackLoops html
clusterTimeProfiles html
consDynamicNet html
createBiopaxnew html
createIntIDs html
findSignalingAxes html
findxneighborsoverlap html
findxnextneighbors html
genGenelists html
genGenelistssub html
genIntIDs html
generate_DSSignalingBase html
genfullConsensusGraph html
getAlias_Ensemble html
getAliasfromSTRINGIDs html
getBiopaxModel html
getConsensusSTRINGIDs html
getDS_PWs html
getDS_TFs html
getDS_TGs html
getFCsplines html
getGenesIntersection html
getOmicsDataset html
getOmicsTimepoints html
getOmicsallGeneIDs html
getOmicsallProteinIDs html
getProteinIntersection html
getSTRING_graph html
getTFIntersection html
getUS_PWs html
getUS_TFs html
getUS_regulators html
get_matching_transcripts html
getbipartitegraphInfo html
gettpIntersection html
identPWsofTFs html
identRegulators html
identTFTGsinPWs html
identTFs html
identifyPR html
identifyPWTFTGs html
identifyPWs html
identifyRsofTFs html
identifyTFs html
infoConsensusGraph html
loadGenelists html
loadPWs html
plotConsDynNet html
plotConsensusGraph html
plotConsensusProfiles html
plotTimeProfileClusters html
predictFCvals html
preparePWinfo html
print.OmicsData html
pwIntOmics-package html
readOmics html
readPWdata html
readPhosphodata html
readTFdata html
readTFtargets html
selectPWsofTFs html
staticConsensusNet html
temp_correlations html
** building package indices
** 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 'pwOmics' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pwOmics' as pwOmics_1.26.0.zip
* DONE (pwOmics)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'pwOmics' successfully unpacked and MD5 sums checked
|
pwOmics.Rcheck/tests_i386/runTests.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("pwOmics")
RUNIT TEST PROTOCOL -- Wed Apr 13 01:10:46 2022
***********************************************
Number of test functions: 0
Number of errors: 0
Number of failures: 0
1 Test Suite :
pwOmics RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
6.03 0.56 6.56
|
pwOmics.Rcheck/tests_x64/runTests.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("pwOmics")
RUNIT TEST PROTOCOL -- Wed Apr 13 01:10:53 2022
***********************************************
Number of test functions: 0
Number of errors: 0
Number of failures: 0
1 Test Suite :
pwOmics RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
6.37 0.53 6.89
|
|
pwOmics.Rcheck/examples_i386/pwOmics-Ex.timings
|
pwOmics.Rcheck/examples_x64/pwOmics-Ex.timings
|