Multiple platform build/check report for BioC 3.20 - INSTALL results for ShortRead on kunpeng2

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4481
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4479
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4359
lconway	macOS 12.7.1 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4539
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	4.4.1 (2024-06-14) -- "Race for Your Life"	4493
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*

INSTALL results for ShortRead on kunpeng2

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

Version: 1.64.0

Command: /home/biocbuild/R/R/bin/R CMD INSTALL ShortRead

StartedAt: 2024-11-19 20:53:15 -0000 (Tue, 19 Nov 2024)

EndedAt: 2024-11-19 20:54:28 -0000 (Tue, 19 Nov 2024)

EllapsedTime: 72.7 seconds

RetCode: 0

Status: OK

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL ShortRead
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘ShortRead’ ...
** using staged installation
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for gzeof in -lz... yes
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking size of unsigned long... 8
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’
using C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c R_init_ShortRead.c -o R_init_ShortRead.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c alphabet.c -o alphabet.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c count.c -o count.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c io.c -o io.o
io.c: In function 'read_prb_as_character':
io.c:227:38: warning: format '%f' expects argument of type 'double', but argument 2 has type 'const char *' [-Wformat=]
  227 |         error("could not read file '%f'", translateChar(STRING_ELT(fname, 0)));
      |                                     ~^
      |                                      |
      |                                      double
      |                                     %s
io.c: In function '_read_solexa_export_file':
io.c:658:49: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'int' [-Wformat=]
  658 |                 error("invalid 'strand' field '%s', %s:%d",
      |                                                ~^
      |                                                 |
      |                                                 char *
      |                                                %d
  659 |                       *elt[13], fname, lineno);
      |                       ~~~~~~~~                   
      |                       |
      |                       int
io.c:676:48: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'int' [-Wformat=]
  676 |             error("invalid 'filtering' field '%s', %s:%d",
      |                                               ~^
      |                                                |
      |                                                char *
      |                                               %d
  677 |                   *elt[21], fname, lineno);
      |                   ~~~~~~~~                      
      |                   |
      |                   int
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c io_bowtie.c -o io_bowtie.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c io_soap.c -o io_soap.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhtslib/include' -I/usr/local/include   -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -fPIC  -g -O2  -Wall  -c readBfaToc.cc -o readBfaToc.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhtslib/include' -I/usr/local/include   -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -fPIC  -g -O2  -Wall  -c read_maq_map.cc -o read_maq_map.o
In file included from read_maq_map.cc:13:
maqmap_m.h: In function 'maqmap_T<max_readlen>* maqmap_read_header(gzFile) [with int max_readlen = 128]':
maqmap_m.h:102:21: warning: pointer 'mm' used after 'void free(void*)' [-Wuse-after-free]
  102 |             Rf_error("MAQ format '%d' not supported", mm->format);
      |             ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void maq_delete_maqmap(maqmap_T<max_readlen>*) [with int max_readlen = 128]',
    inlined from 'void maq_delete_maqmap(maqmap_T<max_readlen>*) [with int max_readlen = 128]' at maqmap_m.h:74:35,
    inlined from 'maqmap_T<max_readlen>* maqmap_read_header(gzFile) [with int max_readlen = 128]' at maqmap_m.h:101:30:
maqmap_m.h:84:14: note: call to 'void free(void*)' here
   84 |     std::free(mm);
      |     ~~~~~~~~~^~~~
maqmap_m.h: In function 'maqmap_T<max_readlen>* maqmap_read_header(gzFile) [with int max_readlen = 64]':
maqmap_m.h:102:21: warning: pointer 'mm' used after 'void free(void*)' [-Wuse-after-free]
  102 |             Rf_error("MAQ format '%d' not supported", mm->format);
      |             ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void maq_delete_maqmap(maqmap_T<max_readlen>*) [with int max_readlen = 64]',
    inlined from 'void maq_delete_maqmap(maqmap_T<max_readlen>*) [with int max_readlen = 64]' at maqmap_m.h:74:35,
    inlined from 'maqmap_T<max_readlen>* maqmap_read_header(gzFile) [with int max_readlen = 64]' at maqmap_m.h:101:30:
maqmap_m.h:84:14: note: call to 'void free(void*)' here
   84 |     std::free(mm);
      |     ~~~~~~~~~^~~~
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c sampler.c -o sampler.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c trim.c -o trim.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c util.c -o util.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c xsnap.c -o xsnap.o
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o ShortRead.so Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o S4Vectors_stubs.o XVector_stubs.o alphabet.o count.o io.o io_bowtie.o io_soap.o readBfaToc.o read_maq_map.o sampler.o trim.o util.o xsnap.o -lz -fopenmp -L/home/biocbuild/R/R-4.4.1/lib -lR
installing to /home/biocbuild/R/R-4.4.1/site-library/00LOCK-ShortRead/00new/ShortRead/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 (ShortRead)