Hervé Pagès
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/SparseArray |
| git_branch: devel |
| git_last_commit: d45d4c3 |
| git_last_commit_date: 2024-02-09 19:09:28 -0400 (Fri, 09 Feb 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:41:21 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 1998/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SparseArray 1.3.4 (landing page) Hervé Pagès
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: SparseArray |
| Version: 1.3.4 |
| Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:SparseArray.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings SparseArray_1.3.4.tar.gz |
| StartedAt: 2024-03-28 09:51:01 -0000 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 09:54:16 -0000 (Thu, 28 Mar 2024) |
| EllapsedTime: 194.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SparseArray.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:SparseArray.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings SparseArray_1.3.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/SparseArray.Rcheck’
* using R Under development (unstable) (2024-03-19 r86153)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SparseArray/DESCRIPTION’ ... OK
* this is package ‘SparseArray’ version ‘1.3.4’
* 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 (GCC) 10.3.1’
* 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 ... OK
* 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 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.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
SVT_SparseArray-class 12.948 1.258 14.235
rowsum-methods 6.540 0.255 6.807
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.19-bioc/meat/SparseArray.Rcheck/00check.log’
for details.
SparseArray.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL SparseArray
###
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* installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library’
* installing *source* package ‘SparseArray’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ExtendableJaggedArray.c -o ExtendableJaggedArray.o
ExtendableJaggedArray.c: In function ‘_move_ExtendableJaggedArrays_to_SVT’:
ExtendableJaggedArray.c:142:4: warning: ‘vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
142 | free(vals);
| ^~~~~~~~~~
ExtendableJaggedArray.c:138:4: warning: ‘offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
138 | free(offs);
| ^~~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c R_init_SparseArray.c -o R_init_SparseArray.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c Rvector_summarization.c -o Rvector_summarization.o
Rvector_summarization.c:1274:12: warning: ‘count_NA_list_elts’ defined but not used [-Wunused-function]
1274 | static int count_NA_list_elts(SEXP x)
| ^~~~~~~~~~~~~~~~~~
Rvector_summarization.c:1262:12: warning: ‘any_NA_list_elt’ defined but not used [-Wunused-function]
1262 | static int any_NA_list_elt(SEXP x)
| ^~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c Rvector_utils.c -o Rvector_utils.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c SBT_utils.c -o SBT_utils.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c SVT_SparseArray_class.c -o SVT_SparseArray_class.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c SparseArray_Complex_methods.c -o SparseArray_Complex_methods.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c SparseArray_Math_methods.c -o SparseArray_Math_methods.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c SparseArray_Ops_methods.c -o SparseArray_Ops_methods.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c SparseArray_abind.c -o SparseArray_abind.o
SparseArray_abind.c: In function ‘REC_abind_SVTs’:
SparseArray_abind.c:157:4: warning: ‘lv_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
157 | copy_Rvector_elts_FUN(lv_vals, 0, ans_vals, k1, lv_len);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SparseArray_abind.c:136:46: note: ‘lv_vals’ was declared here
136 | SEXP SVT, ans, ans_offs, ans_vals, lv_offs, lv_vals;
| ^~~~~~~
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c SparseArray_aperm.c -o SparseArray_aperm.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c SparseArray_class.c -o SparseArray_class.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c SparseArray_dim_tuning.c -o SparseArray_dim_tuning.o
SparseArray_dim_tuning.c: In function ‘REC_tune_SVT’:
SparseArray_dim_tuning.c:260:40: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
260 | if (SVT == R_NilValue || nops == ndim && cumallKEEP[ndim - 1])
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c SparseArray_subassignment.c -o SparseArray_subassignment.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c SparseArray_subsetting.c -o SparseArray_subsetting.o
SparseArray_subsetting.c: In function ‘REC_subset_SVT’:
SparseArray_subsetting.c:139:35: warning: ‘lv_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
139 | build_lookup_table(lookup_table, INTEGER(lv_offs), lv_len);
| ^~~~~~~~~~~~~~~~
SparseArray_subsetting.c:129:7: note: ‘lv_offs’ was declared here
129 | SEXP lv_offs, lv_vals, ans_offs, ans_vals, ans;
| ^~~~~~~
SparseArray_subsetting.c:157:33: warning: ‘lv_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
157 | ans_vals = PROTECT(allocVector(TYPEOF(lv_vals), ans_len));
| ^~~~~~
SparseArray_subsetting.c:129:16: note: ‘lv_vals’ was declared here
129 | SEXP lv_offs, lv_vals, ans_offs, ans_vals, ans;
| ^~~~~~~
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c SparseArray_summarization.c -o SparseArray_summarization.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c SparseMatrix_mult.c -o SparseMatrix_mult.o
SparseMatrix_mult.c:392:13: warning: ‘crossprod2_mat_lv_double’ defined but not used [-Wunused-function]
392 | static void crossprod2_mat_lv_double(const double *mat1, SEXP lv2,
| ^~~~~~~~~~~~~~~~~~~~~~~~
SparseMatrix_mult.c:354:13: warning: ‘crossprod2_lv_mat_double’ defined but not used [-Wunused-function]
354 | static void crossprod2_lv_mat_double(SEXP lv1, const double *mat2,
| ^~~~~~~~~~~~~~~~~~~~~~~~
SparseMatrix_mult.c: In function ‘expand_int_lv’:
SparseMatrix_mult.c:96:24: warning: ‘lv_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
96 | _copy_ints_to_offsets(INTEGER(lv_vals), INTEGER(lv_offs), lv_len, x);
| ^~~~~~~~~~~~~~~~
SparseMatrix_mult.c:96:42: warning: ‘lv_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
96 | _copy_ints_to_offsets(INTEGER(lv_vals), INTEGER(lv_offs), lv_len, x);
| ^~~~~~~~~~~~~~~~
SparseMatrix_mult.c: In function ‘lv_has_no_NA’:
SparseMatrix_mult.c:44:19: warning: ‘lv_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
44 | return has_no_NA(INTEGER(lv_vals), lv_len);
| ^~~~~~~~~~~~~~~~
SparseMatrix_mult.c: In function ‘lv_has_no_NaN_or_Inf’:
SparseMatrix_mult.c:35:27: warning: ‘lv_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
35 | return has_no_NaN_or_Inf(REAL(lv_vals), lv_len);
| ^~~~~~~~~~~~~
SparseMatrix_mult.c: In function ‘expand_double_lv’:
SparseMatrix_mult.c:85:27: warning: ‘lv_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
85 | _copy_doubles_to_offsets(REAL(lv_vals), INTEGER(lv_offs), lv_len, x);
| ^~~~~~~~~~~~~
SparseMatrix_mult.c:85:42: warning: ‘lv_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
85 | _copy_doubles_to_offsets(REAL(lv_vals), INTEGER(lv_offs), lv_len, x);
| ^~~~~~~~~~~~~~~~
SparseMatrix_mult.c: In function ‘C_crossprod2_SVT_SVT’:
SparseMatrix_mult.c:44:19: warning: ‘lv_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
44 | return has_no_NA(INTEGER(lv_vals), lv_len);
| ^~~~~~~~~~~~~~~~
SparseMatrix_mult.c:41:16: note: ‘lv_vals’ was declared here
41 | SEXP lv_offs, lv_vals;
| ^~~~~~~
SparseMatrix_mult.c:44:19: warning: ‘lv_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
44 | return has_no_NA(INTEGER(lv_vals), lv_len);
| ^~~~~~~~~~~~~~~~
SparseMatrix_mult.c:41:16: note: ‘lv_vals’ was declared here
41 | SEXP lv_offs, lv_vals;
| ^~~~~~~
SparseMatrix_mult.c: In function ‘C_crossprod1_SVT’:
SparseMatrix_mult.c:44:19: warning: ‘lv_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
44 | return has_no_NA(INTEGER(lv_vals), lv_len);
| ^~~~~~~~~~~~~~~~
SparseMatrix_mult.c:41:16: note: ‘lv_vals’ was declared here
41 | SEXP lv_offs, lv_vals;
| ^~~~~~~
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c coerceVector2.c -o coerceVector2.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c leaf_vector_Arith.c -o leaf_vector_Arith.o
leaf_vector_Arith.c: In function ‘Rpow_double’:
leaf_vector_Arith.c:164:12: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
164 | if (x < 0 && y == R_PosInf || x == R_NegInf && y != trunc(y))
| ~~~~~~^~~~~~~~~~~~~~~~
leaf_vector_Arith.c: In function ‘mult0_leaf_vector’:
leaf_vector_Arith.c:436:6: warning: ‘lv_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
436 | if (TYPEOF(lv_vals) == INTSXP) {
| ^~~~~~~~~~~~~~~
leaf_vector_Arith.c:434:14: warning: ‘lv_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
434 | lv_offs_p = INTEGER(lv_offs);
| ^~~~~~~~~~~~~~~~
leaf_vector_Arith.c: In function ‘_unary_minus_leaf_vector’:
leaf_vector_Arith.c:94:25: warning: ‘lv_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
94 | double *ans_vals_p = REAL(ans_vals);
| ^~~~~~~~~~~~~~
leaf_vector_Arith.c:109:8: warning: ‘lv_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
109 | ans = _new_leaf_vector(lv_offs, ans_vals);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
leaf_vector_Arith.c: In function ‘_Arith_lv1_v2’:
leaf_vector_Arith.c:384:6: warning: ‘lv1_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
384 | if (TYPEOF(lv1_vals) == INTSXP) {
| ^~~~~~~~~~~~~~~~
leaf_vector_Arith.c:381:12: warning: ‘lv1_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
381 | offs1_p = INTEGER(lv1_offs);
| ^~~~~~~~~~~~~~~~~
leaf_vector_Arith.c: In function ‘_Arith_lv1_lv2’:
leaf_vector_Arith.c:520:7: warning: ‘lv2_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
520 | if (TYPEOF(lv2_vals) == INTSXP) {
| ^~~~~~~~~~~~~~~~
leaf_vector_Arith.c:516:12: warning: ‘lv2_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
516 | offs2_p = INTEGER(lv2_offs);
| ^~~~~~~~~~~~~~~~~
leaf_vector_Arith.c:519:6: warning: ‘lv1_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
519 | if (TYPEOF(lv1_vals) == INTSXP) {
| ^~~~~~~~~~~~~~~~
leaf_vector_Arith.c:515:12: warning: ‘lv1_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
515 | offs1_p = INTEGER(lv1_offs);
| ^~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c leaf_vector_Compare.c -o leaf_vector_Compare.o
leaf_vector_Compare.c: In function ‘Compare_lv1_zero’:
leaf_vector_Compare.c:645:12: warning: ‘lv1_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
645 | offs1, COMPLEX(lv1_vals), lv1_len, Rcomplex0,
| ^~~~~~~~~~~~~~~~~
leaf_vector_Compare.c:626:10: warning: ‘lv1_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
626 | offs1 = INTEGER(lv1_offs);
| ^~~~~~~~~~~~~~~~~
leaf_vector_Compare.c: In function ‘_Compare_lv1_v2’:
leaf_vector_Compare.c:669:10: warning: ‘lv1_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
669 | switch (TYPEOF(lv1_vals)) {
| ^~~~~~~~~~~~~~~~
leaf_vector_Compare.c:668:10: warning: ‘lv1_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
668 | offs1 = INTEGER(lv1_offs);
| ^~~~~~~~~~~~~~~~~
leaf_vector_Compare.c: In function ‘_Compare_lv1_lv2’:
leaf_vector_Compare.c:582:11: warning: ‘lv2_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
582 | Rtype2 = TYPEOF(lv2_vals);
| ^~~~~~~~~~~~~~~~
leaf_vector_Compare.c:576:17: note: ‘lv2_vals’ was declared here
576 | SEXP lv2_offs, lv2_vals;
| ^~~~~~~~
leaf_vector_Compare.c:581:10: warning: ‘lv2_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
581 | offs2 = INTEGER(lv2_offs);
| ^~~~~~~~~~~~~~~~~
leaf_vector_Compare.c:576:7: note: ‘lv2_offs’ was declared here
576 | SEXP lv2_offs, lv2_vals;
| ^~~~~~~~
leaf_vector_Compare.c:542:11: warning: ‘lv2_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
542 | Rtype2 = TYPEOF(lv2_vals);
| ^~~~~~~~~~~~~~~~
leaf_vector_Compare.c:536:17: note: ‘lv2_vals’ was declared here
536 | SEXP lv2_offs, lv2_vals;
| ^~~~~~~~
leaf_vector_Compare.c:541:10: warning: ‘lv2_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
541 | offs2 = INTEGER(lv2_offs);
| ^~~~~~~~~~~~~~~~~
leaf_vector_Compare.c:536:7: note: ‘lv2_offs’ was declared here
536 | SEXP lv2_offs, lv2_vals;
| ^~~~~~~~
leaf_vector_Compare.c:502:11: warning: ‘lv2_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
502 | Rtype2 = TYPEOF(lv2_vals);
| ^~~~~~~~~~~~~~~~
leaf_vector_Compare.c:496:17: note: ‘lv2_vals’ was declared here
496 | SEXP lv2_offs, lv2_vals;
| ^~~~~~~~
leaf_vector_Compare.c:501:10: warning: ‘lv2_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
501 | offs2 = INTEGER(lv2_offs);
| ^~~~~~~~~~~~~~~~~
leaf_vector_Compare.c:496:7: note: ‘lv2_offs’ was declared here
496 | SEXP lv2_offs, lv2_vals;
| ^~~~~~~~
leaf_vector_Compare.c:462:11: warning: ‘lv2_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
462 | Rtype2 = TYPEOF(lv2_vals);
| ^~~~~~~~~~~~~~~~
leaf_vector_Compare.c:456:17: note: ‘lv2_vals’ was declared here
456 | SEXP lv2_offs, lv2_vals;
| ^~~~~~~~
leaf_vector_Compare.c:461:10: warning: ‘lv2_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
461 | offs2 = INTEGER(lv2_offs);
| ^~~~~~~~~~~~~~~~~
leaf_vector_Compare.c:456:7: note: ‘lv2_offs’ was declared here
456 | SEXP lv2_offs, lv2_vals;
| ^~~~~~~~
leaf_vector_Compare.c:720:11: warning: ‘lv1_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
720 | Rtype1 = TYPEOF(lv1_vals);
| ^~~~~~~~~~~~~~~~
leaf_vector_Compare.c:719:10: warning: ‘lv1_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
719 | offs1 = INTEGER(lv1_offs);
| ^~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c leaf_vector_Logic.c -o leaf_vector_Logic.o
leaf_vector_Logic.c: In function ‘_Logic_lv1_lv2’:
leaf_vector_Logic.c:88:23: warning: ‘lv2_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
88 | INTEGER(lv2_offs), INTEGER(lv2_vals), lv2_len,
| ^~~~~~~~~~~~~~~~~
leaf_vector_Logic.c:88:4: warning: ‘lv2_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
88 | INTEGER(lv2_offs), INTEGER(lv2_vals), lv2_len,
| ^~~~~~~~~~~~~~~~~
leaf_vector_Logic.c:87:23: warning: ‘lv1_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
87 | INTEGER(lv1_offs), INTEGER(lv1_vals), lv1_len,
| ^~~~~~~~~~~~~~~~~
leaf_vector_Logic.c:87:4: warning: ‘lv1_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
87 | INTEGER(lv1_offs), INTEGER(lv1_vals), lv1_len,
| ^~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c leaf_vector_dotprod.c -o leaf_vector_dotprod.o
leaf_vector_dotprod.c: In function ‘_dotprod_leaf_vectors’:
leaf_vector_dotprod.c:21:23: warning: ‘lv2_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
21 | INTEGER(lv2_offs), REAL(lv2_vals), lv2_len,
| ^~~~~~~~~~~~~~
leaf_vector_dotprod.c:21:4: warning: ‘lv2_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
21 | INTEGER(lv2_offs), REAL(lv2_vals), lv2_len,
| ^~~~~~~~~~~~~~~~~
leaf_vector_dotprod.c:20:23: warning: ‘lv1_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
20 | INTEGER(lv1_offs), REAL(lv1_vals), lv1_len,
| ^~~~~~~~~~~~~~
leaf_vector_dotprod.c:20:4: warning: ‘lv1_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
20 | INTEGER(lv1_offs), REAL(lv1_vals), lv1_len,
| ^~~~~~~~~~~~~~~~~
leaf_vector_dotprod.c: In function ‘_dotprod_leaf_vector_and_finite_col’:
leaf_vector_dotprod.c:47:12: warning: ‘lv1_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
47 | vals1_p = REAL(lv1_vals);
| ^~~~~~~~~~~~~~
leaf_vector_dotprod.c:46:12: warning: ‘lv1_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
46 | offs1_p = INTEGER(lv1_offs);
| ^~~~~~~~~~~~~~~~~
leaf_vector_dotprod.c: In function ‘_dotprod_leaf_vector_and_double_col’:
leaf_vector_dotprod.c:71:12: warning: ‘lv1_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
71 | vals1_p = REAL(lv1_vals);
| ^~~~~~~~~~~~~~
leaf_vector_dotprod.c:70:12: warning: ‘lv1_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
70 | offs1_p = INTEGER(lv1_offs);
| ^~~~~~~~~~~~~~~~~
leaf_vector_dotprod.c: In function ‘_dotprod_leaf_vector_and_noNA_int_col’:
leaf_vector_dotprod.c:107:12: warning: ‘lv1_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
107 | vals1_p = INTEGER(lv1_vals);
| ^~~~~~~~~~~~~~~~~
leaf_vector_dotprod.c:106:12: warning: ‘lv1_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
106 | offs1_p = INTEGER(lv1_offs);
| ^~~~~~~~~~~~~~~~~
leaf_vector_dotprod.c: In function ‘_dotprod_leaf_vector_and_int_col’:
leaf_vector_dotprod.c:132:12: warning: ‘lv1_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
132 | vals1_p = INTEGER(lv1_vals);
| ^~~~~~~~~~~~~~~~~
leaf_vector_dotprod.c:131:12: warning: ‘lv1_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
131 | offs1_p = INTEGER(lv1_offs);
| ^~~~~~~~~~~~~~~~~
leaf_vector_dotprod.c: In function ‘_dotprod0_leaf_vector’:
leaf_vector_dotprod.c:188:30: warning: ‘lv_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
188 | return _dotprod0_double_col(REAL(lv_vals), lv_len);
| ^~~~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c leaf_vector_summarization.c -o leaf_vector_summarization.o
leaf_vector_summarization.c: In function ‘_summarize_leaf_vector’:
leaf_vector_summarization.c:21:2: warning: ‘lv_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
21 | _summarize_Rvector(lv_vals, summarize_op, res);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c leaf_vector_utils.c -o leaf_vector_utils.o
leaf_vector_utils.c: In function ‘_remove_zeros_from_leaf_vector’:
leaf_vector_utils.c:169:12: warning: ‘lv_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
169 | ans_len = _collect_offsets_of_nonzero_Rsubvec_elts(
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
170 | lv_vals, 0, lv_len,
| ~~~~~~~~~~~~~~~~~~~
171 | offs_buf);
| ~~~~~~~~~
leaf_vector_utils.c:178:22: warning: ‘lv_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
178 | _copy_selected_ints(INTEGER(lv_offs), offs_buf, ans_len,
| ^~~~~~~~~~~~~~~~
leaf_vector_utils.c: In function ‘_coerce_leaf_vector’:
leaf_vector_utils.c:207:36: warning: ‘lv_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
207 | if (_coercion_can_introduce_zeros(TYPEOF(lv_vals), new_Rtype))
| ^~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.4-devel-2024.03.20/include/Rdefines.h:41,
from leaf_vector_utils.h:4,
from leaf_vector_utils.c:4:
/home/biocbuild/R/R-4.4-devel-2024.03.20/include/Rinternals.h:371:20: warning: ‘lv_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
371 | #define PROTECT(s) Rf_protect(s)
| ^~~~~~~~~~
leaf_vector_utils.c:200:7: note: ‘lv_offs’ was declared here
200 | SEXP lv_offs, lv_vals, ans_vals, ans;
| ^~~~~~~
leaf_vector_utils.c: In function ‘_subassign_leaf_vector_with_Rvector’:
leaf_vector_utils.c:239:10: warning: ‘lv_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
239 | Rtype = TYPEOF(lv_vals);
| ^~~~~~~~~~~~~~~
leaf_vector_utils.c:287:12: warning: ‘lv_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
287 | offs1_p = INTEGER(lv_offs);
| ^~~~~~~~~~~~~~~~
leaf_vector_utils.c: In function ‘_lv_apply_to_REALSXP’:
leaf_vector_utils.c:374:13: warning: ‘lv_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
374 | in_Rtype = TYPEOF(lv_vals);
| ^~~~~~~~~~~~~~~
leaf_vector_utils.c:373:9: warning: ‘lv_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
373 | offs = INTEGER(lv_offs);
| ^~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c matrixStats_methods.c -o matrixStats_methods.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c randomSparseArray.c -o randomSparseArray.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c readSparseCSV.c -o readSparseCSV.o
readSparseCSV.c: In function ‘C_readSparseCSV_as_SVT_SparseMatrix’:
readSparseCSV.c:148:3: warning: ‘vals_buf’ may be used uninitialized in this function [-Wmaybe-uninitialized]
148 | IntAE_extend(ae, increase_buflength(ae->_buflength));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readSparseCSV.c:307:20: note: ‘vals_buf’ was declared here
307 | IntAE *offs_buf, *vals_buf;
| ^~~~~~~~
readSparseCSV.c:147:21: warning: ‘offs_buf’ may be used uninitialized in this function [-Wmaybe-uninitialized]
147 | if (ae->_nelt == ae->_buflength)
| ~~^~~~~~~~~~~~
readSparseCSV.c:307:9: note: ‘offs_buf’ was declared here
307 | IntAE *offs_buf, *vals_buf;
| ^~~~~~~~
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c rowsum_methods.c -o rowsum_methods.o
rowsum_methods.c: In function ‘C_rowsum_SVT’:
rowsum_methods.c:109:4: warning: ‘lv_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
109 | INTEGER(lv_vals), INTEGER(lv_offs), lv_len,
| ^~~~~~~~~~~~~~~~
rowsum_methods.c:98:24: note: ‘lv_vals’ was declared here
98 | SEXP subSVT, lv_offs, lv_vals;
| ^~~~~~~
rowsum_methods.c:109:22: warning: ‘lv_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
109 | INTEGER(lv_vals), INTEGER(lv_offs), lv_len,
| ^~~~~~~~~~~~~~~~
rowsum_methods.c:98:15: note: ‘lv_offs’ was declared here
98 | SEXP subSVT, lv_offs, lv_vals;
| ^~~~~~~
rowsum_methods.c:88:4: warning: ‘lv_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
88 | REAL(lv_vals), INTEGER(lv_offs), lv_len,
| ^~~~~~~~~~~~~
rowsum_methods.c:78:24: note: ‘lv_vals’ was declared here
78 | SEXP subSVT, lv_offs, lv_vals;
| ^~~~~~~
rowsum_methods.c:88:19: warning: ‘lv_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
88 | REAL(lv_vals), INTEGER(lv_offs), lv_len,
| ^~~~~~~~~~~~~~~~
rowsum_methods.c:78:15: note: ‘lv_offs’ was declared here
78 | SEXP subSVT, lv_offs, lv_vals;
| ^~~~~~~
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c sparseMatrix_utils.c -o sparseMatrix_utils.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -c test.c -o test.o
gcc -shared -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -L/usr/local/lib -o SparseArray.so ExtendableJaggedArray.o IRanges_stubs.o R_init_SparseArray.o Rvector_summarization.o Rvector_utils.o S4Vectors_stubs.o SBT_utils.o SVT_SparseArray_class.o SparseArray_Complex_methods.o SparseArray_Math_methods.o SparseArray_Ops_methods.o SparseArray_abind.o SparseArray_aperm.o SparseArray_class.o SparseArray_dim_tuning.o SparseArray_subassignment.o SparseArray_subsetting.o SparseArray_summarization.o SparseMatrix_mult.o XVector_stubs.o coerceVector2.o leaf_vector_Arith.o leaf_vector_Compare.o leaf_vector_Logic.o leaf_vector_dotprod.o leaf_vector_summarization.o leaf_vector_utils.o matrixStats_methods.o randomSparseArray.o readSparseCSV.o rowsum_methods.o sparseMatrix_utils.o test.o -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -lR
installing to /home/biocbuild/R/R-4.4-devel-2024.03.20/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 Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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> library(testthat)
> library(SparseArray)
Loading required package: Matrix
Loading required package: BiocGenerics
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, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
union, 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 1 | SKIP 0 | PASS 5894 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 5894 ]
>
> proc.time()
user system elapsed
39.104 2.181 41.386
SparseArray.Rcheck/SparseArray-Ex.timings
| name | user | system | elapsed | |
| COO_SparseArray-class | 0.894 | 0.024 | 0.920 | |
| SVT_SparseArray-class | 12.948 | 1.258 | 14.235 | |
| SparseArray-Complex-methods | 0 | 0 | 0 | |
| SparseArray-Math-methods | 0.008 | 0.000 | 0.008 | |
| SparseArray-Ops-methods | 0.009 | 0.000 | 0.009 | |
| SparseArray-abind | 0.114 | 0.004 | 0.118 | |
| SparseArray-aperm | 0 | 0 | 0 | |
| SparseArray-class | 1.195 | 0.051 | 1.250 | |
| SparseArray-dim-tuning | 0.005 | 0.001 | 0.005 | |
| SparseArray-misc-methods | 0.001 | 0.000 | 0.001 | |
| SparseArray-subassignment | 0.048 | 0.000 | 0.048 | |
| SparseArray-subsetting | 0.200 | 0.019 | 0.223 | |
| SparseArray-summarization | 0.008 | 0.000 | 0.008 | |
| SparseMatrix-mult | 0.042 | 0.004 | 0.046 | |
| extract_sparse_array | 0.084 | 0.012 | 0.096 | |
| matrixStats-methods | 0.053 | 0.016 | 0.070 | |
| randomSparseArray | 3.017 | 0.100 | 3.122 | |
| readSparseCSV | 0.022 | 0.004 | 0.027 | |
| rowsum-methods | 6.540 | 0.255 | 6.807 | |