Aaron Lun
| Snapshot Date: 2025-01-02 13:00 -0500 (Thu, 02 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/diffHic |
| git_branch: RELEASE_3_20 |
| git_last_commit: d60781d |
| git_last_commit_date: 2024-10-29 10:00:57 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-01-09 12:11 -0500 (Thu, 09 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4358 |
| 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 570/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| diffHic 1.38.0 (landing page) Aaron Lun
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the diffHic package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/diffHic.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: diffHic |
| Version: 1.38.0 |
| Command: /home/biocbuild/R/R/bin/R CMD INSTALL diffHic |
| StartedAt: 2025-01-08 20:17:09 -0000 (Wed, 08 Jan 2025) |
| EndedAt: 2025-01-08 20:19:11 -0000 (Wed, 08 Jan 2025) |
| EllapsedTime: 121.7 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/R/R/bin/R CMD INSTALL diffHic
###
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* installing to library ‘/home/biocbuild/R/R-4.4.2/site-library’
* installing *source* package ‘diffHic’ ...
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.2/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.2/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c binner.cpp -o binner.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.2/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.2/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c check_input.cpp -o check_input.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.2/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.2/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c cluster_2d.cpp -o cluster_2d.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.2/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.2/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c count_background.cpp -o count_background.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.2/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.2/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c count_connect.cpp -o count_connect.o
count_connect.cpp: In function ‘SEXPREC* count_connect(SEXP, SEXP)’:
count_connect.cpp:57:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
57 | for (size_t odex=0; odex < ncombos; ++odex) {
| ~~~~~^~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.2/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.2/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c count_patch.cpp -o count_patch.o
count_patch.cpp: In function ‘SEXPREC* count_patch(SEXP, SEXP, SEXP, SEXP, SEXP)’:
count_patch.cpp:45:33: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
45 | for (size_t vecdex=0; vecdex<ncombos; ++vecdex) {
| ~~~~~~^~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.2/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.2/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c directionality.cpp -o directionality.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.2/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.2/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c init.cpp -o init.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.2/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.2/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c iterative_correction.cpp -o iterative_correction.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.2/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.2/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c neighbors.cpp -o neighbors.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.2/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.2/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c pair_stats.cpp -o pair_stats.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.2/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.2/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c quadrant_bg.cpp -o quadrant_bg.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.2/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.2/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c report_hic_pairs.cpp -o report_hic_pairs.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.2/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.2/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c trended_filter.cpp -o trended_filter.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4.2/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4.2/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c utils.cpp -o utils.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o diffHic.so binner.o check_input.o cluster_2d.o count_background.o count_connect.o count_patch.o directionality.o init.o iterative_correction.o neighbors.o pair_stats.o quadrant_bg.o report_hic_pairs.o trended_filter.o utils.o /home/biocbuild/R/R-4.4.2/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-4.4.2/site-library/00LOCK-diffHic/00new/diffHic/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 (diffHic)