Back to Multiple platform build/check report for BioC 3.16
ABC[D]EFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2022-07-04 11:06:02 -0400 (Mon, 04 Jul 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4343
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4148
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4160
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

CHECK results for distinct on palomino4


To the developers/maintainers of the distinct package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 534/2124HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
distinct 1.9.0  (landing page)
Simone Tiberi
Snapshot Date: 2022-07-03 14:00:03 -0400 (Sun, 03 Jul 2022)
git_url: https://git.bioconductor.org/packages/distinct
git_branch: master
git_last_commit: f048022
git_last_commit_date: 2022-04-26 12:04:11 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: distinct
Version: 1.9.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:distinct.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings distinct_1.9.0.tar.gz
StartedAt: 2022-07-04 01:07:31 -0400 (Mon, 04 Jul 2022)
EndedAt: 2022-07-04 01:13:05 -0400 (Mon, 04 Jul 2022)
EllapsedTime: 334.6 seconds
RetCode: 0
Status:   OK  
CheckDir: distinct.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:distinct.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings distinct_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/distinct.Rcheck'
* using R version 4.2.0 Patched (2022-06-02 r82447 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'distinct/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'distinct' version '1.9.0'
* 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 'distinct' 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
* 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 ... 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 for x64 is not available
File 'F:/biocbuild/bbs-3.16-bioc/R/library/distinct/libs/x64/distinct.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
distinct_test  2.3   0.01   63.61
* 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: 3 NOTEs
See
  'F:/biocbuild/bbs-3.16-bioc/meat/distinct.Rcheck/00check.log'
for details.



Installation output

distinct.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/distinct_1.9.0.tar.gz && rm -rf distinct.buildbin-libdir && mkdir distinct.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=distinct.buildbin-libdir distinct_1.9.0.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL distinct_1.9.0.zip && rm distinct_1.9.0.tar.gz distinct_1.9.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0 1181k    0 10723    0     0   281k      0  0:00:04 --:--:--  0:00:04  283k
100 1181k  100 1181k    0     0  4014k      0 --:--:-- --:--:-- --:--:-- 4017k
only one architecture so ignoring '--merge-multiarch'
* installing *source* package 'distinct' ...
** using staged installation
** libs
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rfast/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Perm.cpp -o Perm.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rfast/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Perm_covariates.cpp -o Perm_covariates.o
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/Rfast/include/Rfast.h:5,
                 from Perm_covariates.cpp:2:
F:/biocbuild/bbs-3.16-bioc/R/library/Rfast/include/Rfast/matrix.hpp:553: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  553 |     #pragma omp parallel for
      | 
F:/biocbuild/bbs-3.16-bioc/R/library/Rfast/include/Rfast/matrix.hpp:604: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  604 |     #pragma omp parallel for
      | 
F:/biocbuild/bbs-3.16-bioc/R/library/Rfast/include/Rfast/matrix.hpp:621: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  621 |       #pragma omp parallel for
      | 
F:/biocbuild/bbs-3.16-bioc/R/library/Rfast/include/Rfast/matrix.hpp:639: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  639 |           #pragma omp parallel for
      | 
F:/biocbuild/bbs-3.16-bioc/R/library/Rfast/include/Rfast/matrix.hpp:654: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  654 |       #pragma omp parallel for
      | 
F:/biocbuild/bbs-3.16-bioc/R/library/Rfast/include/Rfast/matrix.hpp:669: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  669 |           #pragma omp parallel for
      | 
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"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rfast/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Perm_covariates_parallel.cpp -o Perm_covariates_parallel.o
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/Rfast/include/Rfast.h:5,
                 from Perm_covariates_parallel.cpp:2:
F:/biocbuild/bbs-3.16-bioc/R/library/Rfast/include/Rfast/matrix.hpp:553: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  553 |     #pragma omp parallel for
      | 
F:/biocbuild/bbs-3.16-bioc/R/library/Rfast/include/Rfast/matrix.hpp:604: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  604 |     #pragma omp parallel for
      | 
F:/biocbuild/bbs-3.16-bioc/R/library/Rfast/include/Rfast/matrix.hpp:621: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  621 |       #pragma omp parallel for
      | 
F:/biocbuild/bbs-3.16-bioc/R/library/Rfast/include/Rfast/matrix.hpp:639: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  639 |           #pragma omp parallel for
      | 
F:/biocbuild/bbs-3.16-bioc/R/library/Rfast/include/Rfast/matrix.hpp:654: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  654 |       #pragma omp parallel for
      | 
F:/biocbuild/bbs-3.16-bioc/R/library/Rfast/include/Rfast/matrix.hpp:669: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  669 |           #pragma omp parallel for
      | 
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"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rfast/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Perm_parallel.cpp -o Perm_parallel.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rfast/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++ -shared -s -static-libgcc -o distinct.dll tmp.def Perm.o Perm_covariates.o Perm_covariates_parallel.o Perm_parallel.o RcppExports.o -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.16-bioc/meat/distinct.buildbin-libdir/00LOCK-distinct/00new/distinct/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'distinct' as distinct_1.9.0.zip
* DONE (distinct)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'distinct' successfully unpacked and MD5 sums checked

Tests output

distinct.Rcheck/tests/testthat.Rout


R version 4.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics"
Copyright (C) 2022 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(distinct)
> test_check("distinct")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ]
> 
> proc.time()
   user  system elapsed 
  10.37    0.84   75.14 

Example timings

distinct.Rcheck/distinct-Ex.timings

nameusersystemelapsed
Kang_subset000
distinct_test 2.30 0.0163.61
log2_FC0.20.00.2
plot_cdfs0.690.070.75
plot_densities0.750.010.76
res000
top_results0.250.000.25