Simone Tiberi
| Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/distinct |
| git_branch: RELEASE_3_17 |
| git_last_commit: 3f26450 |
| git_last_commit_date: 2023-05-15 05:46:56 -0400 (Mon, 15 May 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:35:19 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 | ||||
| Package 566/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| distinct 1.12.2 (landing page) Simone Tiberi
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the distinct package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/distinct.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: distinct |
| Version: 1.12.2 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:distinct.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings distinct_1.12.2.tar.gz |
| StartedAt: 2023-10-15 20:52:08 -0400 (Sun, 15 Oct 2023) |
| EndedAt: 2023-10-15 21:00:44 -0400 (Sun, 15 Oct 2023) |
| EllapsedTime: 516.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: distinct.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:distinct.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings distinct_1.12.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/distinct.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘distinct/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘distinct’ version ‘1.12.2’
* 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 ‘distinct’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
installed size is 5.4Mb
sub-directories of 1Mb or more:
data 1.0Mb
libs 4.1Mb
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘Rfast’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
perm_test_parallel_R: no visible binding for global variable ‘cl_id’
perm_test_parallel_covariates_R: no visible binding for global variable
‘cl_id’
plot_cdfs: no visible binding for global variable ‘group’
plot_densities: no visible binding for global variable ‘group’
Undefined global functions or variables:
cl_id group
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... 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
distinct_test 1.489 0.156 72.669
* 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 ...
‘distinct.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 5 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/distinct.Rcheck/00check.log’
for details.
distinct.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL distinct
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘distinct’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include' -I/usr/local/include -fpic -g -O2 -Wall -c Perm.cpp -o Perm.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include' -I/usr/local/include -fpic -g -O2 -Wall -c Perm_covariates.cpp -o Perm_covariates.o
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:16,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast.h:5,
from Perm_covariates.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/helpers.hpp:19: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
19 | #pragma omp critical
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/helpers.hpp:92: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
92 | #pragma omp critical
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/helpers.hpp:105: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
105 | #pragma omp critical
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/helpers.hpp:157: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
157 | #pragma omp critical
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/helpers.hpp:164: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
164 | #pragma omp critical
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/helpers.hpp:175: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
175 | #pragma omp critical
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/helpers.hpp:182: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
182 | #pragma omp critical
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/helpers.hpp:193: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
193 | #pragma omp critical
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/helpers.hpp:200: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
200 | #pragma omp critical
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/helpers.hpp:211: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
211 | #pragma omp critical
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/helpers.hpp:218: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
218 | #pragma omp critical
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/helpers.hpp:228: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
228 | #pragma omp critical
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/helpers.hpp:456: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
456 | #pragma omp critical
|
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast.h:5,
from Perm_covariates.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:939: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
939 | #pragma omp parallel for
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:944: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
944 | #pragma omp critical
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:973: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
973 | #pragma omp parallel for
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:978: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
978 | #pragma omp critical
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:1006: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
1006 | #pragma omp parallel for
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:1011: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
1011 | #pragma omp critical
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:1394: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
1394 | #pragma omp parallel for
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:1416: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
1416 | #pragma omp parallel for
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:1421: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
1421 | #pragma omp critical
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:1498: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
1498 | #pragma omp parallel for
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:1520: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
1520 | #pragma omp parallel for
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:1525: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
1525 | #pragma omp critical
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:1556: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
1556 | #pragma omp parallel for
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:1579: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
1579 | #pragma omp parallel for
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:1600: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
1600 | #pragma omp parallel for
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:1621: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
1621 | #pragma omp parallel for
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:1762: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
1762 | #pragma omp critical
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:1823: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
1823 | #pragma omp critical
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:1884: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
1884 | #pragma omp critical
|
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:15,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast.h:5,
from Perm_covariates.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/types.hpp:42:17: warning: inline variables are only available with ‘-std=c++17’ or ‘-std=gnu++17’
42 | inline static type val;
| ^~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/types.hpp:47:17: warning: inline variables are only available with ‘-std=c++17’ or ‘-std=gnu++17’
47 | inline static type val= NA_INTEGER;
| ^~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/types.hpp:52:17: warning: inline variables are only available with ‘-std=c++17’ or ‘-std=gnu++17’
52 | inline static type val= NA_LOGICAL;
| ^~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/types.hpp:57:17: warning: inline variables are only available with ‘-std=c++17’ or ‘-std=gnu++17’
57 | inline static type val= NA_REAL;
| ^~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/types.hpp:62:17: warning: inline variables are only available with ‘-std=c++17’ or ‘-std=gnu++17’
62 | inline static type val = NA_STRING;
| ^~~~~~
Perm_covariates.cpp: In function ‘arma::vec my_rint_reg(const mat&, const vec&, Rcpp::IntegerVector, const unsigned int&, const unsigned int&, const double&, const unsigned int&)’:
Perm_covariates.cpp:189:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
189 | for(int i=0;i<p;i++)
| ~^~
Perm_covariates.cpp:210:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
210 | while(i++<maxiters && sum(abs(b2-b1.col(0))) > tol) {
| ~~~^~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include' -I/usr/local/include -fpic -g -O2 -Wall -c Perm_covariates_parallel.cpp -o Perm_covariates_parallel.o
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:16,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast.h:5,
from Perm_covariates_parallel.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/helpers.hpp:19: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
19 | #pragma omp critical
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/helpers.hpp:92: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
92 | #pragma omp critical
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/helpers.hpp:105: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
105 | #pragma omp critical
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/helpers.hpp:157: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
157 | #pragma omp critical
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/helpers.hpp:164: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
164 | #pragma omp critical
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/helpers.hpp:175: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
175 | #pragma omp critical
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/helpers.hpp:182: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
182 | #pragma omp critical
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/helpers.hpp:193: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
193 | #pragma omp critical
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/helpers.hpp:200: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
200 | #pragma omp critical
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/helpers.hpp:211: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
211 | #pragma omp critical
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/helpers.hpp:218: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
218 | #pragma omp critical
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/helpers.hpp:228: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
228 | #pragma omp critical
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/helpers.hpp:456: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
456 | #pragma omp critical
|
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast.h:5,
from Perm_covariates_parallel.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:939: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
939 | #pragma omp parallel for
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:944: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
944 | #pragma omp critical
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:973: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
973 | #pragma omp parallel for
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:978: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
978 | #pragma omp critical
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:1006: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
1006 | #pragma omp parallel for
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:1011: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
1011 | #pragma omp critical
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:1394: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
1394 | #pragma omp parallel for
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:1416: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
1416 | #pragma omp parallel for
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:1421: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
1421 | #pragma omp critical
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:1498: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
1498 | #pragma omp parallel for
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:1520: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
1520 | #pragma omp parallel for
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:1525: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
1525 | #pragma omp critical
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:1556: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
1556 | #pragma omp parallel for
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:1579: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
1579 | #pragma omp parallel for
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:1600: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
1600 | #pragma omp parallel for
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:1621: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
1621 | #pragma omp parallel for
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:1762: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
1762 | #pragma omp critical
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:1823: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
1823 | #pragma omp critical
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:1884: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
1884 | #pragma omp critical
|
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:15,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast.h:5,
from Perm_covariates_parallel.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/types.hpp:42:17: warning: inline variables are only available with ‘-std=c++17’ or ‘-std=gnu++17’
42 | inline static type val;
| ^~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/types.hpp:47:17: warning: inline variables are only available with ‘-std=c++17’ or ‘-std=gnu++17’
47 | inline static type val= NA_INTEGER;
| ^~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/types.hpp:52:17: warning: inline variables are only available with ‘-std=c++17’ or ‘-std=gnu++17’
52 | inline static type val= NA_LOGICAL;
| ^~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/types.hpp:57:17: warning: inline variables are only available with ‘-std=c++17’ or ‘-std=gnu++17’
57 | inline static type val= NA_REAL;
| ^~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/types.hpp:62:17: warning: inline variables are only available with ‘-std=c++17’ or ‘-std=gnu++17’
62 | inline static type val = NA_STRING;
| ^~~~~~
Perm_covariates_parallel.cpp: In function ‘arma::vec my_rint_reg_parallel(const mat&, const vec&, Rcpp::IntegerVector, const unsigned int&, const unsigned int&, const double&, const unsigned int&)’:
Perm_covariates_parallel.cpp:189:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
189 | for(int i=0;i<p;i++)
| ~^~
Perm_covariates_parallel.cpp:210:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
210 | while(i++<maxiters && sum(abs(b2-b1.col(0))) > tol) {
| ~~~^~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include' -I/usr/local/include -fpic -g -O2 -Wall -c Perm_parallel.cpp -o Perm_parallel.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o distinct.so Perm.o Perm_covariates.o Perm_covariates_parallel.o Perm_parallel.o RcppExports.o -llapack -L/home/biocbuild/bbs-3.17-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-distinct/00new/distinct/libs
** R
** data
** 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 (distinct)
distinct.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 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.
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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
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> library(testthat)
> library(distinct)
> test_check("distinct")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 8 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 8 ]
>
> proc.time()
user system elapsed
10.674 0.929 83.916
distinct.Rcheck/distinct-Ex.timings
| name | user | system | elapsed | |
| Kang_subset | 0.000 | 0.000 | 0.001 | |
| distinct_test | 1.489 | 0.156 | 72.669 | |
| log2_FC | 0.935 | 0.152 | 1.087 | |
| plot_cdfs | 0.518 | 0.012 | 0.530 | |
| plot_densities | 0.555 | 0.068 | 0.622 | |
| res | 0.001 | 0.000 | 0.000 | |
| top_results | 0.210 | 0.012 | 0.222 | |