Steffi Grote
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/GOfuncR |
| Branch: RELEASE_3_9 |
| Last Commit: 2f633dc |
| Last Changed Date: 2019-05-02 11:54:10 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:40:10 -0400 (Wed, 16 Oct 2019).
| Package 693/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GOfuncR 1.4.0 Steffi Grote
| 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 | |
| Package: GOfuncR |
| Version: 1.4.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GOfuncR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GOfuncR_1.4.0.tar.gz |
| StartedAt: 2019-10-16 04:07:57 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 04:24:37 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 1000.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GOfuncR.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:GOfuncR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GOfuncR_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/GOfuncR.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GOfuncR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GOfuncR' version '1.4.0'
* 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 'GOfuncR' 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 ... OK
* 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 R/sysdata.rda ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/GOfuncR/libs/i386/GOfuncR.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/GOfuncR/libs/x64/GOfuncR.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plot_anno_scores 20.47 1.47 21.95
go_enrich 13.93 0.58 14.56
get_anno_categories 10.92 0.72 11.70
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plot_anno_scores 14.08 0.86 14.93
get_anno_categories 10.67 0.38 11.05
go_enrich 9.38 0.45 9.85
* 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: 1 NOTE
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/GOfuncR.Rcheck/00check.log'
for details.
GOfuncR.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/GOfuncR_1.4.0.tar.gz && rm -rf GOfuncR.buildbin-libdir && mkdir GOfuncR.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GOfuncR.buildbin-libdir GOfuncR_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL GOfuncR_1.4.0.zip && rm GOfuncR_1.4.0.tar.gz GOfuncR_1.4.0.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 3149k 100 3149k 0 0 33.3M 0 --:--:-- --:--:-- --:--:-- 36.1M
install for i386
* installing *source* package 'GOfuncR' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c binom_categorytest.cc -o binom_categorytest.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c binom_randset.cc -o binom_randset.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c blocks.cpp -o blocks.o
blocks.cpp: In function 'std::set rannum_blocks(std::vector, std::vector, const std::map, int>&, std::vector)':
blocks.cpp:30:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j=0; j < candidate_bed.size(); j++){
^
blocks.cpp:34:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int k=0; k < background.size(); k++){
^
blocks.cpp:68:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int g=0; g rannum_genelen(int, const std::map, int>&, std::vector, long int)':
ran_genelen.cpp:19:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while (random_numbers.size() < n_candidate) {
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c read_bed.cpp -o read_bed.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c roll.cpp -o roll.o
roll.cpp: In function 'std::set rannum_roll(std::vector, std::vector, const std::map, int>&, std::vector)':
roll.cpp:30:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j=0; j < candidate_bed.size(); j++){
^
roll.cpp:36:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i < background_bed.size(); i++){
^
roll.cpp:92:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int g=0; g rannum_blocks(std::vector, std::vector, const std::map, int>&, std::vector)':
blocks.cpp:30:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j=0; j < candidate_bed.size(); j++){
^
blocks.cpp:34:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int k=0; k < background.size(); k++){
^
blocks.cpp:68:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int g=0; g rannum_genelen(int, const std::map, int>&, std::vector, long int)':
ran_genelen.cpp:19:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while (random_numbers.size() < n_candidate) {
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c read_bed.cpp -o read_bed.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c roll.cpp -o roll.o
roll.cpp: In function 'std::set rannum_roll(std::vector, std::vector, const std::map, int>&, std::vector)':
roll.cpp:30:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j=0; j < candidate_bed.size(); j++){
^
roll.cpp:36:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i < background_bed.size(); i++){
^
roll.cpp:92:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int g=0; g
|
GOfuncR.Rcheck/tests_i386/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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)
> library(GOfuncR)
Loading required package: vioplot
Loading required package: sm
Package 'sm', version 2.2-5.6: type help(sm) for summary information
Loading required package: zoo
Attaching package: 'zoo'
The following objects are masked from 'package:base':
as.Date, as.Date.numeric
>
> test_check("GOfuncR")
== testthat results ===========================================================
[ OK: 60 | SKIPPED: 0 | WARNINGS: 6 | FAILED: 0 ]
>
> proc.time()
user system elapsed
336.31 59.78 405.86
|
GOfuncR.Rcheck/tests_x64/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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)
> library(GOfuncR)
Loading required package: vioplot
Loading required package: sm
Package 'sm', version 2.2-5.6: type help(sm) for summary information
Loading required package: zoo
Attaching package: 'zoo'
The following objects are masked from 'package:base':
as.Date, as.Date.numeric
>
> test_check("GOfuncR")
== testthat results ===========================================================
[ OK: 60 | SKIPPED: 0 | WARNINGS: 6 | FAILED: 0 ]
>
> proc.time()
user system elapsed
275.01 59.34 334.90
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GOfuncR.Rcheck/examples_i386/GOfuncR-Ex.timings
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GOfuncR.Rcheck/examples_x64/GOfuncR-Ex.timings
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