Li Shen, Mount Sinai
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/GeneOverlap |
| Branch: RELEASE_3_8 |
| Last Commit: 0750179 |
| Last Changed Date: 2018-10-30 11:41:52 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:23:29 -0400 (Sat, 13 Apr 2019).
| Package 601/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GeneOverlap 1.18.0 Li Shen, Mount Sinai
| 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: GeneOverlap |
| Version: 1.18.0 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneOverlap.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings GeneOverlap_1.18.0.tar.gz |
| StartedAt: 2019-04-13 02:28:20 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 02:29:54 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 94.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GeneOverlap.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:GeneOverlap.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings GeneOverlap_1.18.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/GeneOverlap.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 'GeneOverlap/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GeneOverlap' version '1.18.0'
* 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 'GeneOverlap' 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
drawHeatmap,GeneOverlapMatrix: no visible global function definition
for 'p.adjust'
print,GeneOverlap: no visible global function definition for 'head'
testGeneOverlap,GeneOverlap: no visible global function definition for
'setNames'
Undefined global functions or variables:
head p.adjust setNames
Consider adding
importFrom("stats", "p.adjust", "setNames")
importFrom("utils", "head")
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' ... NOTE
The following files look like leftovers/mistakes:
'Rplots.pdf'
Please remove them from your package.
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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 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/GeneOverlap.Rcheck/00check.log'
for details.
GeneOverlap.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/GeneOverlap_1.18.0.tar.gz && rm -rf GeneOverlap.buildbin-libdir && mkdir GeneOverlap.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GeneOverlap.buildbin-libdir GeneOverlap_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL GeneOverlap_1.18.0.zip && rm GeneOverlap_1.18.0.tar.gz GeneOverlap_1.18.0.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 162k 100 162k 0 0 5410k 0 --:--:-- --:--:-- --:--:-- 6268k
install for i386
* installing *source* package 'GeneOverlap' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'GeneOverlap'
finding HTML links ... done
GeneOverlap-package html
GeneOverlap html
GeneOverlapMatrix html
drawHeatmap html
getGenomeSize html
getList html
getReadonly html
getReadonlyMatrix html
gs.RNASeq html
hESC.ChIPSeq.list html
hESC.RNASeq.list html
newGOM html
newGeneOverlap html
testGeneOverlap html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'GeneOverlap' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GeneOverlap' as GeneOverlap_1.18.0.zip
* DONE (GeneOverlap)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'GeneOverlap' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
GeneOverlap.Rcheck/tests_i386/runTests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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("GeneOverlap")
RUNIT TEST PROTOCOL -- Sat Apr 13 02:29:48 2019
***********************************************
Number of test functions: 2
Number of errors: 0
Number of failures: 0
1 Test Suite :
GeneOverlap RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2
Number of errors: 0
Number of failures: 0
Warning messages:
1: In getPval(go.obj) : Test has not been performed yet.
2: In getOddsRatio(go.obj) : Test has not been performed yet.
>
> proc.time()
user system elapsed
0.57 0.04 0.62
|
GeneOverlap.Rcheck/tests_x64/runTests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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("GeneOverlap")
RUNIT TEST PROTOCOL -- Sat Apr 13 02:29:50 2019
***********************************************
Number of test functions: 2
Number of errors: 0
Number of failures: 0
1 Test Suite :
GeneOverlap RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2
Number of errors: 0
Number of failures: 0
Warning messages:
1: In getPval(go.obj) : Test has not been performed yet.
2: In getOddsRatio(go.obj) : Test has not been performed yet.
>
> proc.time()
user system elapsed
0.68 0.10 0.79
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GeneOverlap.Rcheck/examples_i386/GeneOverlap-Ex.timings
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GeneOverlap.Rcheck/examples_x64/GeneOverlap-Ex.timings
|