Aimin Yan
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/PathwaySplice |
| Branch: master |
| Last Commit: 8eac434 |
| Last Changed Date: 2019-01-04 13:43:03 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 12:34:01 -0400 (Tue, 09 Apr 2019).
| Package 1157/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| PathwaySplice 1.7.1 Aimin Yan
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: PathwaySplice |
| Version: 1.7.1 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PathwaySplice.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings PathwaySplice_1.7.1.tar.gz |
| StartedAt: 2019-04-09 04:48:12 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 05:09:49 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 1296.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: PathwaySplice.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PathwaySplice.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings PathwaySplice_1.7.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/PathwaySplice.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PathwaySplice/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PathwaySplice' version '1.7.1'
* 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 'PathwaySplice' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
.onAttach: no visible global function definition for 'winMenuAddItem'
compareResults2: no visible global function definition for 'ggplot'
compareResults2: no visible global function definition for 'aes'
compareResults2: no visible binding for global variable
'random_sampling_200k'
compareResults2: no visible binding for global variable 'PValue'
compareResults2: no visible binding for global variable 'PathwaySplice'
compareResults2: no visible global function definition for 'geom_point'
compareResults2: no visible global function definition for
'geom_smooth'
compareResults2: no visible global function definition for 'labs'
compareResults2: no visible global function definition for
'scale_colour_manual'
compareResults2: no visible global function definition for
'scale_shape_manual'
netplot: no visible global function definition for 'get.col.scale'
Undefined global functions or variables:
PValue PathwaySplice aes geom_point geom_smooth get.col.scale ggplot
labs random_sampling_200k scale_colour_manual scale_shape_manual
winMenuAddItem
Consider adding
importFrom("utils", "winMenuAddItem")
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 or elapsed time > 5s
user system elapsed
enrichmentMap 51.64 1.89 53.60
compareResults 45.21 2.69 49.10
runPathwaySplice 38.79 1.60 40.49
makeGeneTable 18.48 0.90 19.39
lrTestBias 18.09 1.21 19.29
gmtGene2Cat 11.32 0.23 11.63
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
enrichmentMap 52.73 2.99 55.83
runPathwaySplice 47.81 2.10 50.02
compareResults 44.64 2.28 48.11
lrTestBias 15.64 0.00 15.64
makeGeneTable 15.06 0.05 15.11
gmtGene2Cat 13.81 0.23 14.22
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.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-3.9-bioc/meat/PathwaySplice.Rcheck/00check.log'
for details.
PathwaySplice.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/PathwaySplice_1.7.1.tar.gz && rm -rf PathwaySplice.buildbin-libdir && mkdir PathwaySplice.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PathwaySplice.buildbin-libdir PathwaySplice_1.7.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL PathwaySplice_1.7.1.zip && rm PathwaySplice_1.7.1.tar.gz PathwaySplice_1.7.1.zip
###
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0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
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100 2291k 100 2291k 0 0 7659k 0 --:--:-- --:--:-- --:--:-- 7795k
install for i386
* installing *source* package 'PathwaySplice' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'PathwaySplice'
finding HTML links ... done
compareResults html
enrichmentMap html
featureBasedData html
gmtGene2Cat html
lrTestBias html
makeGeneTable html
outKegg2Gmt html
runPathwaySplice 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 'PathwaySplice' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PathwaySplice' as PathwaySplice_1.7.1.zip
* DONE (PathwaySplice)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'PathwaySplice' successfully unpacked and MD5 sums checked
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PathwaySplice.Rcheck/tests_i386/testthat.Rout
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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.
> library(testthat)
> test_check("PathwaySplice")
Loading required package: PathwaySplice
[1] "P-value from logistic regression is 3.98e-205"
== testthat results ===========================================================
OK: 12 SKIPPED: 1 FAILED: 0
>
> proc.time()
user system elapsed
218.48 7.50 227.73
|
PathwaySplice.Rcheck/tests_x64/testthat.Rout
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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.
> library(testthat)
> test_check("PathwaySplice")
Loading required package: PathwaySplice
[1] "P-value from logistic regression is 3.98e-205"
== testthat results ===========================================================
OK: 12 SKIPPED: 1 FAILED: 0
>
> proc.time()
user system elapsed
223.20 11.06 239.28
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PathwaySplice.Rcheck/examples_i386/PathwaySplice-Ex.timings
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PathwaySplice.Rcheck/examples_x64/PathwaySplice-Ex.timings
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