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This page was generated on 2024-12-24 11:40 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 1994/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SparseArray 1.7.2  (landing page)
Hervé Pagès
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/SparseArray
git_branch: devel
git_last_commit: 49e375d
git_last_commit_date: 2024-11-14 03:44:42 -0500 (Thu, 14 Nov 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for SparseArray on nebbiolo1

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.

raw results


Summary

Package: SparseArray
Version: 1.7.2
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:SparseArray.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings SparseArray_1.7.2.tar.gz
StartedAt: 2024-12-24 02:24:26 -0500 (Tue, 24 Dec 2024)
EndedAt: 2024-12-24 02:28:53 -0500 (Tue, 24 Dec 2024)
EllapsedTime: 267.3 seconds
RetCode: 0
Status:   OK  
CheckDir: SparseArray.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:SparseArray.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings SparseArray_1.7.2.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/SparseArray.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘SparseArray/DESCRIPTION’ ... OK
* this is package ‘SparseArray’ version ‘1.7.2’
* 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:
  COO_SparseArray-class.Rd: dgCMatrix-class, lgCMatrix-class
  NaArray-class.Rd: Array
  SVT_SparseArray-class.Rd: dgCMatrix-class, lgCMatrix-class,
    CsparseMatrix-class
  SparseArray-class.Rd: dgCMatrix-class, dgRMatrix-class,
    lgCMatrix-class
  extract_sparse_array.Rd: dgCMatrix-class
  is_nonzero.Rd: dgCMatrix-class, lgCMatrix-class, ngCMatrix-class
  readSparseCSV.Rd: dgCMatrix-class
  read_block_as_sparse.Rd: dgCMatrix-class
  rowsum-methods.Rd: dgCMatrix-class
  sparseMatrix-utils.Rd: dgCMatrix-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: ‘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        38.648  0.676  33.027
SVT_SparseArray-class 12.837  1.818  14.657
rowsum-methods         6.297  0.677   6.976
* 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-3.21-bioc/meat/SparseArray.Rcheck/00check.log’
for details.


Installation output

SparseArray.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL SparseArray
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘SparseArray’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1 -fopenmp -fpic  -g -O2  -Wall -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 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1 -fopenmp -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1 -fopenmp -fpic  -g -O2  -Wall -c OPBufTree.c -o OPBufTree.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1 -fopenmp -fpic  -g -O2  -Wall -c R_init_SparseArray.c -o R_init_SparseArray.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1 -fopenmp -fpic  -g -O2  -Wall -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 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1 -fopenmp -fpic  -g -O2  -Wall -c Rvector_utils.c -o Rvector_utils.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1 -fopenmp -fpic  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1 -fopenmp -fpic  -g -O2  -Wall -c SBT_utils.c -o SBT_utils.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1 -fopenmp -fpic  -g -O2  -Wall -c SVT_SparseArray_class.c -o SVT_SparseArray_class.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1 -fopenmp -fpic  -g -O2  -Wall -c SparseArray_Arith_methods.c -o SparseArray_Arith_methods.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1 -fopenmp -fpic  -g -O2  -Wall -c SparseArray_Compare_methods.c -o SparseArray_Compare_methods.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1 -fopenmp -fpic  -g -O2  -Wall -c SparseArray_Complex_methods.c -o SparseArray_Complex_methods.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1 -fopenmp -fpic  -g -O2  -Wall -c SparseArray_Logic_methods.c -o SparseArray_Logic_methods.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1 -fopenmp -fpic  -g -O2  -Wall -c SparseArray_Math_methods.c -o SparseArray_Math_methods.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1 -fopenmp -fpic  -g -O2  -Wall -c SparseArray_abind.c -o SparseArray_abind.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1 -fopenmp -fpic  -g -O2  -Wall -c SparseArray_aperm.c -o SparseArray_aperm.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1 -fopenmp -fpic  -g -O2  -Wall -c SparseArray_dim_tuning.c -o SparseArray_dim_tuning.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1 -fopenmp -fpic  -g -O2  -Wall -c SparseArray_matrixStats.c -o SparseArray_matrixStats.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1 -fopenmp -fpic  -g -O2  -Wall -c SparseArray_misc_methods.c -o SparseArray_misc_methods.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1 -fopenmp -fpic  -g -O2  -Wall -c SparseArray_subassignment.c -o SparseArray_subassignment.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1 -fopenmp -fpic  -g -O2  -Wall -c SparseArray_subassignment_OLD.c -o SparseArray_subassignment_OLD.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1 -fopenmp -fpic  -g -O2  -Wall -c SparseArray_subsetting.c -o SparseArray_subsetting.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1 -fopenmp -fpic  -g -O2  -Wall -c SparseArray_summarization.c -o SparseArray_summarization.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1 -fopenmp -fpic  -g -O2  -Wall -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 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1 -fopenmp -fpic  -g -O2  -Wall -c SparseVec.c -o SparseVec.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1 -fopenmp -fpic  -g -O2  -Wall -c SparseVec_Arith.c -o SparseVec_Arith.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1 -fopenmp -fpic  -g -O2  -Wall -c SparseVec_Compare.c -o SparseVec_Compare.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1 -fopenmp -fpic  -g -O2  -Wall -c SparseVec_Logic.c -o SparseVec_Logic.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1 -fopenmp -fpic  -g -O2  -Wall -c SparseVec_Math.c -o SparseVec_Math.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1 -fopenmp -fpic  -g -O2  -Wall -c SparseVec_dotprod.c -o SparseVec_dotprod.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1 -fopenmp -fpic  -g -O2  -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1 -fopenmp -fpic  -g -O2  -Wall -c argcheck_utils.c -o argcheck_utils.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1 -fopenmp -fpic  -g -O2  -Wall -c coerceVector2.c -o coerceVector2.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1 -fopenmp -fpic  -g -O2  -Wall -c leaf_utils.c -o leaf_utils.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1 -fopenmp -fpic  -g -O2  -Wall -c randomSparseArray.c -o randomSparseArray.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1 -fopenmp -fpic  -g -O2  -Wall -c readSparseCSV.c -o readSparseCSV.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1 -fopenmp -fpic  -g -O2  -Wall -c rowsum_methods.c -o rowsum_methods.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1 -fopenmp -fpic  -g -O2  -Wall -c sparseMatrix_utils.c -o sparseMatrix_utils.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1 -fopenmp -fpic  -g -O2  -Wall -c test.c -o test.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1 -fopenmp -fpic  -g -O2  -Wall -c thread_control.c -o thread_control.o
gcc -shared -L/home/biocbuild/bbs-3.21-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-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-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)

Tests output

SparseArray.Rcheck/tests/testthat.Rout


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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 26846 ]
> 
> proc.time()
   user  system elapsed 
 83.752   2.809  84.171 

Example timings

SparseArray.Rcheck/SparseArray-Ex.timings

nameusersystemelapsed
COO_SparseArray-class1.7470.0601.807
NaArray-Arith-methods0.0790.0090.088
NaArray-Compare-methods0.0200.0020.021
NaArray-Logic-methods0.0270.0040.031
NaArray-Math-methods0.0120.0040.016
NaArray-abind000
NaArray-aperm0.0010.0000.000
NaArray-class0.2260.0510.277
NaArray-matrixStats0.0000.0010.001
NaArray-misc-methods0.0730.0060.079
NaArray-subsetting0.1420.0060.148
NaArray-summarization0.0210.0010.022
SVT_SparseArray-class12.837 1.81814.657
SparseArray-Arith-methods0.0670.0090.074
SparseArray-Compare-methods0.0090.0020.012
SparseArray-Complex-methods000
SparseArray-Logic-methods0.0160.0020.018
SparseArray-Math-methods0.0060.0000.006
SparseArray-abind0.0850.0040.090
SparseArray-aperm0.0000.0000.001
SparseArray-class2.3710.3462.718
SparseArray-matrixStats0.0700.0030.052
SparseArray-misc-methods0.1050.0020.103
SparseArray-subassignment0.0350.0030.038
SparseArray-subsetting0.1570.0040.162
SparseArray-summarization0.0280.0010.028
SparseMatrix-mult0.0570.0070.042
extract_sparse_array0.0710.0040.069
is_nonna0.0030.0020.005
is_nonzero0.0040.0010.006
randomSparseArray3.3520.3463.699
readSparseCSV0.0210.0030.023
rowsum-methods6.2970.6776.976
thread-control38.648 0.67633.027