Steffi Grote
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/GOfuncR |
| Branch: RELEASE_3_11 |
| Last Commit: 9eefca3 |
| Last Changed Date: 2020-04-27 15:12:39 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:54:53 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE GOfuncR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 750/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GOfuncR 1.8.0 Steffi Grote
| malbec2 | Linux (Ubuntu 18.04.4 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: GOfuncR |
| Version: 1.8.0 |
| Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:GOfuncR.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings GOfuncR_1.8.0.tar.gz |
| StartedAt: 2020-10-17 01:53:09 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 01:59:13 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 364.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GOfuncR.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:GOfuncR.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings GOfuncR_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/GOfuncR.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GOfuncR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GOfuncR’ version ‘1.8.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘GOfuncR’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 10.8Mb
sub-directories of 1Mb or more:
R 2.0Mb
libs 8.7Mb
* 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
* 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
refine 38.659 0.978 39.443
plot_anno_scores 14.141 0.671 14.731
get_anno_categories 10.334 0.657 13.566
go_enrich 8.298 0.271 8.545
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
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
‘/home/biocbuild/bbs-3.11-bioc/meat/GOfuncR.Rcheck/00check.log’
for details.
GOfuncR.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL GOfuncR
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘GOfuncR’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c binom_categorytest.cc -o binom_categorytest.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c binom_randset.cc -o binom_randset.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c blocks.cpp -o blocks.o
blocks.cpp: In function ‘std::set<int> rannum_blocks(std::vector<bed_str>, std::vector<bed_str>, const std::map<std::__cxx11::basic_string<char>, int>&, std::vector<gen_pos_str>)’:
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<genes_pos.size(); g++){
~^~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c conti_categorytest.cc -o conti_categorytest.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c conti_randset.cc -o conti_randset.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c gene.cc -o gene.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c gene_binom.cc -o gene_binom.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c gene_conti.cc -o gene_conti.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c genes.cc -o genes.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c genes_binom.cc -o genes_binom.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c genes_conti.cc -o genes_conti.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c go.cc -o go.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c go_graph.cc -o go_graph.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c go_graph_binom.cc -o go_graph_binom.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c go_graph_conti.cc -o go_graph_conti.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c go_graph_hyper.cc -o go_graph_hyper.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c go_groups.cc -o go_groups.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c go_groups_binom.cc -o go_groups_binom.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c go_groups_conti.cc -o go_groups_conti.o
go_groups_conti.cc: In member function ‘int* go_groups_conti::calculate_data(std::__cxx11::string&, std::ostream*)’:
go_groups_conti.cc:71:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for ( int idx=0 ; idx < names.size() ; ++idx ) {
~~~~^~~~~~~~~~~~~~
go_groups_conti.cc: In member function ‘int* go_groups_conti::calculate_rand(std::__cxx11::string&, std::ostream*)’:
go_groups_conti.cc:172:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for ( int idx=0 ; idx < names.size() ; ++idx ) {
~~~~^~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c go_groups_hyper.cc -o go_groups_hyper.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c go_obj.cc -o go_obj.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c go_obj_binom.cc -o go_obj_binom.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c go_obj_conti.cc -o go_obj_conti.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c go_obj_hyper.cc -o go_obj_hyper.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c hyper_categorytest.cc -o hyper_categorytest.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c hyper_randset.cc -o hyper_randset.o
hyper_randset.cc: In function ‘void hyper_randset(std::__cxx11::string, int, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, bool)’:
hyper_randset.cc:217:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while (random_numbers.size() < n_candidate) {
~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c idmap.cc -o idmap.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c ran_genelen.cpp -o ran_genelen.o
ran_genelen.cpp: In function ‘std::set<int> rannum_genelen(int, const std::map<std::__cxx11::basic_string<char>, int>&, std::vector<gen_pos_str>, long int)’:
ran_genelen.cpp:19:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while (random_numbers.size() < n_candidate) {
~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c read_bed.cpp -o read_bed.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c roll.cpp -o roll.o
roll.cpp: In function ‘std::set<int> rannum_roll(std::vector<bed_str>, std::vector<bed_str>, const std::map<std::__cxx11::basic_string<char>, int>&, std::vector<gen_pos_str>)’:
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<genes_pos.size(); g++){
~^~~~~~~~~~~~~~~~~
roll.cpp:106:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if ((k == background_bed.size()) || (background_bed[k].chrom != ran_chrom)){
~~^~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c transitions.cc -o transitions.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c unlock_environment.cc -o unlock_environment.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c wilcox_categorytest.cc -o wilcox_categorytest.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c wilcox_randset.cc -o wilcox_randset.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o GOfuncR.so RcppExports.o binom_categorytest.o binom_randset.o blocks.o conti_categorytest.o conti_randset.o gene.o gene_binom.o gene_conti.o genes.o genes_binom.o genes_conti.o go.o go_graph.o go_graph_binom.o go_graph_conti.o go_graph_hyper.o go_groups.o go_groups_binom.o go_groups_conti.o go_groups_hyper.o go_obj.o go_obj_binom.o go_obj_conti.o go_obj_hyper.o hyper_categorytest.o hyper_randset.o idmap.o init.o ran_genelen.o read_bed.o roll.o transitions.o unlock_environment.o wilcox_categorytest.o wilcox_randset.o -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-GOfuncR/00new/GOfuncR/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GOfuncR)
GOfuncR.Rcheck/tests/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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: 73 | SKIPPED: 0 | WARNINGS: 6 | FAILED: 0 ]
>
> proc.time()
user system elapsed
152.601 4.897 159.593
GOfuncR.Rcheck/GOfuncR-Ex.timings
| name | user | system | elapsed | |
| get_anno_categories | 10.334 | 0.657 | 13.566 | |
| get_anno_genes | 1.951 | 0.105 | 2.037 | |
| get_child_nodes | 0.085 | 0.000 | 0.085 | |
| get_ids | 0.303 | 0.003 | 0.306 | |
| get_names | 0.038 | 0.001 | 0.038 | |
| get_parent_nodes | 0.101 | 0.008 | 0.110 | |
| go_enrich | 8.298 | 0.271 | 8.545 | |
| plot_anno_scores | 14.141 | 0.671 | 14.731 | |
| refine | 38.659 | 0.978 | 39.443 | |