Hervé Pagès
| Snapshot Date: 2025-10-24 13:45 -0400 (Fri, 24 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/SparseArray |
| git_branch: devel |
| git_last_commit: 2dd1bf9 |
| git_last_commit_date: 2025-08-28 22:55:59 -0400 (Thu, 28 Aug 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-25 12:04 -0400 (Sat, 25 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4901 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4691 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4658 |
| 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 2072/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SparseArray 1.9.1 (landing page) Hervé Pagès
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | NA | NA | ||||||||||
|
To the developers/maintainers of the SparseArray package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SparseArray.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. |
| Package: SparseArray |
| Version: 1.9.1 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:SparseArray.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings SparseArray_1.9.1.tar.gz |
| StartedAt: 2025-10-25 04:23:59 -0400 (Sat, 25 Oct 2025) |
| EndedAt: 2025-10-25 04:28:34 -0400 (Sat, 25 Oct 2025) |
| EllapsedTime: 274.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SparseArray.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:SparseArray.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings SparseArray_1.9.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/SparseArray.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘SparseArray/DESCRIPTION’ ... OK
* this is package ‘SparseArray’ version ‘1.9.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SparseArray’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
rowsum-methods.Rd: dsparseMatrix-class, dgCMatrix-class,
dgTMatrix-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘SparseArray/libs/SparseArray.so’:
Found non-API calls to R: ‘DATAPTR’, ‘R_GetConnection’,
‘R_ReadConnection’
Compiled code should not call non-API entry points in R.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
thread-control 35.756 0.525 30.482
SVT_SparseArray-class 11.765 1.721 13.489
rowsum-methods 5.738 0.669 6.409
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.22-bioc/meat/SparseArray.Rcheck/00check.log’
for details.
SparseArray.Rcheck/00install.out
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### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL SparseArray
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘SparseArray’ ...
** this is package ‘SparseArray’ version ‘1.9.1’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c ExtendableJaggedArray.c -o ExtendableJaggedArray.o
ExtendableJaggedArray.c: In function ‘_move_ExtendableJaggedArrays_to_SVT’:
ExtendableJaggedArray.c:129:25: warning: ‘nzvals_p’ may be used uninitialized [-Wmaybe-uninitialized]
129 | free(nzvals_p);
| ^~~~~~~~~~~~~~
ExtendableJaggedArray.c:111:22: note: ‘nzvals_p’ was declared here
111 | int *nzvals_p, *nzoffs_p;
| ^~~~~~~~
ExtendableJaggedArray.c:125:25: warning: ‘nzoffs_p’ may be used uninitialized [-Wmaybe-uninitialized]
125 | free(nzoffs_p);
| ^~~~~~~~~~~~~~
ExtendableJaggedArray.c:111:33: note: ‘nzoffs_p’ was declared here
111 | int *nzvals_p, *nzoffs_p;
| ^~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c OPBufTree.c -o OPBufTree.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c R_init_SparseArray.c -o R_init_SparseArray.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c Rvector_summarization.c -o Rvector_summarization.o
Rvector_summarization.c:1370:12: warning: ‘count_NA_list_elts’ defined but not used [-Wunused-function]
1370 | static int count_NA_list_elts(SEXP x)
| ^~~~~~~~~~~~~~~~~~
Rvector_summarization.c:1360:12: warning: ‘any_NA_list_elt’ defined but not used [-Wunused-function]
1360 | static int any_NA_list_elt(SEXP x)
| ^~~~~~~~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c Rvector_utils.c -o Rvector_utils.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c SBT_utils.c -o SBT_utils.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c SVT_SparseArray_class.c -o SVT_SparseArray_class.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c SparseArray_Arith_methods.c -o SparseArray_Arith_methods.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c SparseArray_Compare_methods.c -o SparseArray_Compare_methods.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c SparseArray_Complex_methods.c -o SparseArray_Complex_methods.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c SparseArray_Logic_methods.c -o SparseArray_Logic_methods.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c SparseArray_Math_methods.c -o SparseArray_Math_methods.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c SparseArray_abind.c -o SparseArray_abind.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c SparseArray_aperm.c -o SparseArray_aperm.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c SparseArray_dim_tuning.c -o SparseArray_dim_tuning.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c SparseArray_matrixStats.c -o SparseArray_matrixStats.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c SparseArray_misc_methods.c -o SparseArray_misc_methods.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c SparseArray_subassignment.c -o SparseArray_subassignment.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c SparseArray_subassignment_OLD.c -o SparseArray_subassignment_OLD.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c SparseArray_subsetting.c -o SparseArray_subsetting.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c SparseArray_summarization.c -o SparseArray_summarization.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c SparseMatrix_mult.c -o SparseMatrix_mult.o
SparseMatrix_mult.c:346:13: warning: ‘crossprod2_doublemat_doubleSV’ defined but not used [-Wunused-function]
346 | static void crossprod2_doublemat_doubleSV(
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SparseMatrix_mult.c:306:13: warning: ‘crossprod2_doubleSV_doublemat’ defined but not used [-Wunused-function]
306 | static void crossprod2_doubleSV_doublemat(
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c SparseVec.c -o SparseVec.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c SparseVec_Arith.c -o SparseVec_Arith.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c SparseVec_Compare.c -o SparseVec_Compare.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c SparseVec_Logic.c -o SparseVec_Logic.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c SparseVec_Math.c -o SparseVec_Math.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c SparseVec_dotprod.c -o SparseVec_dotprod.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c XVector_stubs.c -o XVector_stubs.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c argcheck_utils.c -o argcheck_utils.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c coerceVector2.c -o coerceVector2.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c leaf_utils.c -o leaf_utils.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c randomSparseArray.c -o randomSparseArray.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c readSparseCSV.c -o readSparseCSV.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c rowsum_methods.c -o rowsum_methods.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c sparseMatrix_utils.c -o sparseMatrix_utils.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c test.c -o test.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c thread_control.c -o thread_control.o
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o SparseArray.so ExtendableJaggedArray.o IRanges_stubs.o OPBufTree.o R_init_SparseArray.o Rvector_summarization.o Rvector_utils.o S4Vectors_stubs.o SBT_utils.o SVT_SparseArray_class.o SparseArray_Arith_methods.o SparseArray_Compare_methods.o SparseArray_Complex_methods.o SparseArray_Logic_methods.o SparseArray_Math_methods.o SparseArray_abind.o SparseArray_aperm.o SparseArray_dim_tuning.o SparseArray_matrixStats.o SparseArray_misc_methods.o SparseArray_subassignment.o SparseArray_subassignment_OLD.o SparseArray_subsetting.o SparseArray_summarization.o SparseMatrix_mult.o SparseVec.o SparseVec_Arith.o SparseVec_Compare.o SparseVec_Logic.o SparseVec_Math.o SparseVec_dotprod.o XVector_stubs.o argcheck_utils.o coerceVector2.o leaf_utils.o randomSparseArray.o readSparseCSV.o rowsum_methods.o sparseMatrix_utils.o test.o thread_control.o -fopenmp -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-SparseArray/00new/SparseArray/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 (SparseArray)
SparseArray.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
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Platform: x86_64-pc-linux-gnu
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Type 'license()' or 'licence()' for distribution details.
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> library(testthat)
> library(SparseArray)
Loading required package: Matrix
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:Matrix':
expand, unname
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: S4Arrays
Loading required package: abind
Loading required package: IRanges
Attaching package: 'S4Arrays'
The following object is masked from 'package:abind':
abind
The following object is masked from 'package:base':
rowsum
>
> test_check("SparseArray")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 28672 ]
>
> proc.time()
user system elapsed
89.812 3.487 91.159
SparseArray.Rcheck/SparseArray-Ex.timings
| name | user | system | elapsed | |
| COO_SparseArray-class | 1.512 | 0.054 | 1.566 | |
| NaArray-Arith-methods | 0.078 | 0.002 | 0.081 | |
| NaArray-Compare-methods | 0.019 | 0.000 | 0.019 | |
| NaArray-Logic-methods | 0.028 | 0.000 | 0.028 | |
| NaArray-Math-methods | 0.013 | 0.000 | 0.013 | |
| NaArray-abind | 0 | 0 | 0 | |
| NaArray-aperm | 0 | 0 | 0 | |
| NaArray-class | 0.222 | 0.050 | 0.271 | |
| NaArray-matrixStats | 0 | 0 | 0 | |
| NaArray-misc-methods | 0.069 | 0.000 | 0.069 | |
| NaArray-subsetting | 0.13 | 0.00 | 0.13 | |
| NaArray-summarization | 0.018 | 0.001 | 0.019 | |
| SVT_SparseArray-class | 11.765 | 1.721 | 13.489 | |
| SparseArray-Arith-methods | 0.065 | 0.003 | 0.068 | |
| SparseArray-Compare-methods | 0.010 | 0.000 | 0.009 | |
| SparseArray-Complex-methods | 0 | 0 | 0 | |
| SparseArray-Logic-methods | 0.016 | 0.000 | 0.015 | |
| SparseArray-Math-methods | 0.004 | 0.001 | 0.004 | |
| SparseArray-abind | 0.080 | 0.000 | 0.079 | |
| SparseArray-aperm | 0 | 0 | 0 | |
| SparseArray-class | 2.397 | 0.327 | 2.725 | |
| SparseArray-matrixStats | 0.071 | 0.002 | 0.052 | |
| SparseArray-misc-methods | 0.101 | 0.001 | 0.097 | |
| SparseArray-subassignment | 0.037 | 0.000 | 0.038 | |
| SparseArray-subsetting | 0.155 | 0.000 | 0.155 | |
| SparseArray-summarization | 0.026 | 0.001 | 0.028 | |
| SparseMatrix-mult | 0.052 | 0.001 | 0.037 | |
| extract_sparse_array | 0.070 | 0.002 | 0.065 | |
| is_nonna | 0.003 | 0.000 | 0.003 | |
| is_nonzero | 0.002 | 0.001 | 0.003 | |
| randomSparseArray | 3.381 | 0.311 | 3.692 | |
| readSparseCSV | 0.019 | 0.000 | 0.020 | |
| rowsum-methods | 5.738 | 0.669 | 6.409 | |
| thread-control | 35.756 | 0.525 | 30.482 | |