Back to Multiple platform build/check report for BioC 3.19:   simplified   long
ABCDEFGH[I]JKLMNOPQRSTUVWXYZ

This page was generated on 2024-03-28 11:40:52 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4426
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 1048/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IRISFGM 1.11.1  (landing page)
Yuzhou Chang
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/IRISFGM
git_branch: devel
git_last_commit: e63c932
git_last_commit_date: 2024-01-12 08:38:28 -0400 (Fri, 12 Jan 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    ERROR  skipped
palomino3Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    ERROR  skipped

INSTALL results for IRISFGM on kunpeng2


To the developers/maintainers of the IRISFGM package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/IRISFGM.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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: IRISFGM
Version: 1.11.1
Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL IRISFGM
StartedAt: 2024-03-27 20:31:39 -0000 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 20:33:30 -0000 (Wed, 27 Mar 2024)
EllapsedTime: 110.5 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL IRISFGM
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library’
* installing *source* package ‘IRISFGM’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
using C++ compiler: ‘g++ (GCC) 10.3.1’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -DVER=2.08 -fPIC  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -DVER=2.08 -fPIC  -g -O2  -Wall  -c cluster.cpp -o cluster.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -DVER=2.08 -fPIC  -g -O2  -Wall  -c expand.cpp -o expand.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -DVER=2.08 -fPIC  -g -O2  -Wall  -c get_options.cpp -o get_options.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c getline.c -o getline.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -DVER=2.08 -fPIC  -g -O2  -Wall  -c main.cpp -o main.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -DVER=2.08 -fPIC  -g -O2  -Wall  -c make_graph.cpp -o make_graph.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -DVER=2.08 -fPIC  -g -O2  -Wall  -c rcpp_irisfgm.cpp -o rcpp_irisfgm.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -DVER=2.08 -fPIC  -g -O2  -Wall  -c read_array.cpp -o read_array.o
read_array.cpp: In function ‘void discretize_new(const char*)’:
read_array.cpp:882:26: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘__gnu_cxx::__alloc_traits<std::allocator<long unsigned int>, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=]
  882 |         fprintf(F2, "%s_%d", genes_n[id], eflags[id][i]);
      |                         ~^
      |                          |
      |                          int
      |                         %ld
read_array.cpp:883:35: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  883 |         for (std::size_t j = 0; j < cols; j++) {
      |                                 ~~^~~~~~
read_array.cpp: In function ‘void discretize_rpkm(const char*)’:
read_array.cpp:1376:26: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘__gnu_cxx::__alloc_traits<std::allocator<long unsigned int>, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=]
 1376 |         fprintf(F2, "%s_%d", genes_n[id], eflags[id][i]);
      |                         ~^
      |                          |
      |                          int
      |                         %ld
read_array.cpp:1377:35: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
 1377 |         for (std::size_t j = 0; j < cols; j++) {
      |                                 ~~^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -DVER=2.08 -fPIC  -g -O2  -Wall  -c struct.cpp -o struct.o
struct.cpp: In function ‘void uglyTime(const char*, ...)’:
struct.cpp:75:15: warning: variable ‘lastTime’ set but not used [-Wunused-but-set-variable]
   75 |   static long lastTime = 0;
      |               ^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -DVER=2.08 -fPIC  -g -O2  -Wall  -c write_block.cpp -o write_block.o
g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -L/usr/local/lib -o IRISFGM.so RcppExports.o cluster.o expand.o get_options.o getline.o main.o make_graph.o rcpp_irisfgm.o read_array.o struct.o write_block.o -fopenmp -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -lR
installing to /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/00LOCK-IRISFGM/00new/IRISFGM/libs
** R
** data
** byte-compile and prepare package for lazy loading
Creating a generic function from function ‘ReadFrom10X_h5’ in package ‘IRISFGM’
Creating a generic function from function ‘ReadFrom10X_folder’ in package ‘IRISFGM’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'IRISFGM' is deprecated and will be removed from Bioconductor
  version 3.20
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'IRISFGM' is deprecated and will be removed from Bioconductor
  version 3.20
** testing if installed package keeps a record of temporary installation path
* DONE (IRISFGM)