Back to Multiple platform build/check report for BioC 3.19:   simplified   long
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-06-11 14:39 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4522
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4468
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 136/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
batchelor 1.20.0  (landing page)
Aaron Lun
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/batchelor
git_branch: RELEASE_3_19
git_last_commit: d14eff8
git_last_commit_date: 2024-04-30 11:13:32 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


INSTALL results for batchelor on nebbiolo1

To the developers/maintainers of the batchelor package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/batchelor.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.

raw results


Summary

Package: batchelor
Version: 1.20.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL batchelor
StartedAt: 2024-06-09 15:51:16 -0400 (Sun, 09 Jun 2024)
EndedAt: 2024-06-09 15:52:02 -0400 (Sun, 09 Jun 2024)
EllapsedTime: 46.2 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL batchelor
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘batchelor’ ...
** 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-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-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-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c adjust_shift_variance.cpp -o adjust_shift_variance.o
adjust_shift_variance.cpp: In function ‘Rcpp::NumericVector adjust_shift_variance(Rcpp::NumericMatrix, Rcpp::NumericMatrix, Rcpp::NumericMatrix, double, Rcpp::IntegerVector, Rcpp::IntegerVector)’:
adjust_shift_variance.cpp:34:16: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘int’ [-Wsign-compare]
   34 |     if (ngenes != data2.nrow() || ngenes != vect.ncol()) {
      |         ~~~~~~~^~~~~~~~~~~~~~~
adjust_shift_variance.cpp:34:42: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘int’ [-Wsign-compare]
   34 |     if (ngenes != data2.nrow() || ngenes != vect.ncol()) {
      |                                   ~~~~~~~^~~~~~~~~~~~~~
adjust_shift_variance.cpp:39:16: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘int’ [-Wsign-compare]
   39 |     if (ncells != vect.nrow()) {
      |         ~~~~~~~^~~~~~~~~~~~~~
adjust_shift_variance.cpp:118:39: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  118 |             for (size_t other=0; other<restrict1.size(); ++other) {
      |                                  ~~~~~^~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c find_mutual_nns.cpp -o find_mutual_nns.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c smooth_gaussian_kernel.cpp -o smooth_gaussian_kernel.o
smooth_gaussian_kernel.cpp: In function ‘SEXPREC* smooth_gaussian_kernel(Rcpp::NumericMatrix, Rcpp::IntegerVector, Rcpp::NumericMatrix, double)’:
smooth_gaussian_kernel.cpp:18:13: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   18 |     if (nmnn!=index.size()) {
      |         ~~~~^~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c utils.cpp -o utils.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o batchelor.so RcppExports.o adjust_shift_variance.o find_mutual_nns.o smooth_gaussian_kernel.o utils.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-batchelor/00new/batchelor/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 (batchelor)