Nicholas Cooley
| Snapshot Date: 2025-01-20 13:40 -0500 (Mon, 20 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/SynExtend |
| git_branch: devel |
| git_last_commit: 34a29be |
| git_last_commit_date: 2025-01-16 11:36:07 -0500 (Thu, 16 Jan 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-21 11:47 -0500 (Tue, 21 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4777 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4502 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4467 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4422 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4406 |
| 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 2100/2286 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SynExtend 1.19.3 (landing page) Nicholas Cooley
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | ERROR | ERROR | skipped | skipped | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the SynExtend package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SynExtend.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. |
| Package: SynExtend |
| Version: 1.19.3 |
| Command: /home/biocbuild/R/R/bin/R CMD INSTALL SynExtend |
| StartedAt: 2025-01-20 19:42:17 -0000 (Mon, 20 Jan 2025) |
| EndedAt: 2025-01-20 19:42:54 -0000 (Mon, 20 Jan 2025) |
| EllapsedTime: 37.5 seconds |
| RetCode: 0 |
| Status: OK |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD INSTALL SynExtend
###
##############################################################################
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* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘SynExtend’ ...
** using staged installation
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
using Fortran compiler: ‘GNU Fortran (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c CDend.c -o CDend.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c CShuffle.c -o CShuffle.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c HungarianAlgo.c -o HungarianAlgo.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c LoserTree.c -o LoserTree.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c MoranI.c -o MoranI.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c NucleotideCounts.c -o NucleotideCounts.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c OnDiskLP.c -o OnDiskLP.o
OnDiskLP.c: In function ‘kway_mergesort_file_inplace’:
OnDiskLP.c:656:31: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint_fast64_t’ {aka ‘long unsigned int’} [-Wformat=]
656 | Rprintf("\tIteration %llu of %llu (%6.01f%% complete, used ",
| ~~~^
| |
| long long unsigned int
| %lu
657 | tmpniter, nmax_iterations, cur_progress);
| ~~~~~~~~
| |
| uint_fast64_t {aka long unsigned int}
OnDiskLP.c:656:39: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint_fast64_t’ {aka ‘long unsigned int’} [-Wformat=]
656 | Rprintf("\tIteration %llu of %llu (%6.01f%% complete, used ",
| ~~~^
| |
| long long unsigned int
| %lu
657 | tmpniter, nmax_iterations, cur_progress);
| ~~~~~~~~~~~~~~~
| |
| uint_fast64_t {aka long unsigned int}
OnDiskLP.c:717:37: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint_fast64_t’ {aka ‘long unsigned int’} [-Wformat=]
717 | Rprintf("\tIteration %llu of %llu (%6.01f%% complete, used ",
| ~~~^
| |
| long long unsigned int
| %lu
718 | tmpniter, nmax_iterations, cur_progress);
| ~~~~~~~~
| |
| uint_fast64_t {aka long unsigned int}
OnDiskLP.c:717:45: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint_fast64_t’ {aka ‘long unsigned int’} [-Wformat=]
717 | Rprintf("\tIteration %llu of %llu (%6.01f%% complete, used ",
| ~~~^
| |
| long long unsigned int
| %lu
718 | tmpniter, nmax_iterations, cur_progress);
| ~~~~~~~~~~~~~~~
| |
| uint_fast64_t {aka long unsigned int}
OnDiskLP.c:743:37: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint_fast64_t’ {aka ‘long unsigned int’} [-Wformat=]
743 | Rprintf("\tIteration %llu of %llu (%6.01f%% complete, used ",
| ~~~^
| |
| long long unsigned int
| %lu
744 | tmpniter, nmax_iterations, cur_progress);
| ~~~~~~~~
| |
| uint_fast64_t {aka long unsigned int}
OnDiskLP.c:743:45: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint_fast64_t’ {aka ‘long unsigned int’} [-Wformat=]
743 | Rprintf("\tIteration %llu of %llu (%6.01f%% complete, used ",
| ~~~^
| |
| long long unsigned int
| %lu
744 | tmpniter, nmax_iterations, cur_progress);
| ~~~~~~~~~~~~~~~
| |
| uint_fast64_t {aka long unsigned int}
OnDiskLP.c: In function ‘kway_mergesort_file’:
OnDiskLP.c:834:31: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint_fast64_t’ {aka ‘long unsigned int’} [-Wformat=]
834 | Rprintf("\tIteration %llu of %llu (%6.01f%% complete, used ",
| ~~~^
| |
| long long unsigned int
| %lu
835 | tmpniter, nmax_iterations, cur_progress);
| ~~~~~~~~
| |
| uint_fast64_t {aka long unsigned int}
OnDiskLP.c:834:39: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint_fast64_t’ {aka ‘long unsigned int’} [-Wformat=]
834 | Rprintf("\tIteration %llu of %llu (%6.01f%% complete, used ",
| ~~~^
| |
| long long unsigned int
| %lu
835 | tmpniter, nmax_iterations, cur_progress);
| ~~~~~~~~~~~~~~~
| |
| uint_fast64_t {aka long unsigned int}
OnDiskLP.c:895:37: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint_fast64_t’ {aka ‘long unsigned int’} [-Wformat=]
895 | Rprintf("\tIteration %llu of %llu (%6.01f%% complete, used ",
| ~~~^
| |
| long long unsigned int
| %lu
896 | tmpniter, nmax_iterations, cur_progress);
| ~~~~~~~~
| |
| uint_fast64_t {aka long unsigned int}
OnDiskLP.c:895:45: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint_fast64_t’ {aka ‘long unsigned int’} [-Wformat=]
895 | Rprintf("\tIteration %llu of %llu (%6.01f%% complete, used ",
| ~~~^
| |
| long long unsigned int
| %lu
896 | tmpniter, nmax_iterations, cur_progress);
| ~~~~~~~~~~~~~~~
| |
| uint_fast64_t {aka long unsigned int}
OnDiskLP.c:914:35: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint_fast64_t’ {aka ‘long unsigned int’} [-Wformat=]
914 | Rprintf("\tIteration %llu of %llu (%6.01f%% complete, used ",
| ~~~^
| |
| long long unsigned int
| %lu
915 | tmpniter, nmax_iterations, cur_progress);
| ~~~~~~~~
| |
| uint_fast64_t {aka long unsigned int}
OnDiskLP.c:914:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint_fast64_t’ {aka ‘long unsigned int’} [-Wformat=]
914 | Rprintf("\tIteration %llu of %llu (%6.01f%% complete, used ",
| ~~~^
| |
| long long unsigned int
| %lu
915 | tmpniter, nmax_iterations, cur_progress);
| ~~~~~~~~~~~~~~~
| |
| uint_fast64_t {aka long unsigned int}
OnDiskLP.c:936:29: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint_fast64_t’ {aka ‘long unsigned int’} [-Wformat=]
936 | Rprintf("\tIteration %llu of %llu (%6.01f%% complete, used ",
| ~~~^
| |
| long long unsigned int
| %lu
937 | tmpniter, nmax_iterations, cur_progress);
| ~~~~~~~~
| |
| uint_fast64_t {aka long unsigned int}
OnDiskLP.c:936:37: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint_fast64_t’ {aka ‘long unsigned int’} [-Wformat=]
936 | Rprintf("\tIteration %llu of %llu (%6.01f%% complete, used ",
| ~~~^
| |
| long long unsigned int
| %lu
937 | tmpniter, nmax_iterations, cur_progress);
| ~~~~~~~~~~~~~~~
| |
| uint_fast64_t {aka long unsigned int}
In function ‘update_node_cluster’,
inlined from ‘cluster_file’ at OnDiskLP.c:1691:5:
OnDiskLP.c:1598:9: warning: ‘max_weight’ may be used uninitialized [-Wmaybe-uninitialized]
1598 | if(max_weight < cur_weight){
| ^
OnDiskLP.c: In function ‘cluster_file’:
OnDiskLP.c:1588:10: note: ‘max_weight’ was declared here
1588 | double max_weight, cur_weight=0, cur_error=0;
| ^~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c PrefixTrie.c -o PrefixTrie.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c R_init_synextend.c -o R_init_synextend.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c RandomForest.c -o RandomForest.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c SEutils.c -o SEutils.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c XORRand.c -o XORRand.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gfortran -fPIC -g -O2 -Wall -Werror=format-security -c _fortran_tabulate.f95 -o _fortran_tabulate.o
f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gfortran -fPIC -g -O2 -Wall -Werror=format-security -c _fortran_utils.f95 -o _fortran_utils.o
f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c calcMIR2C.c -o calcMIR2C.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gfortran -fPIC -g -O2 -Wall -Werror=format-security -c cart_fort.f95 -o cart_fort.o
f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c dendrapply.c -o dendrapply.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o SynExtend.so CDend.o CShuffle.o HungarianAlgo.o LoserTree.o MoranI.o NucleotideCounts.o OnDiskLP.o PrefixTrie.o R_init_synextend.o RandomForest.o SEutils.o XORRand.o _fortran_tabulate.o _fortran_utils.o calcMIR2C.o cart_fort.o dendrapply.o -fopenmp -lgfortran -lm -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-SynExtend/00new/SynExtend/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 (SynExtend)