Hervé Pagès
| Snapshot Date: 2025-11-19 13:40 -0500 (Wed, 19 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/SparseArray |
| git_branch: devel |
| git_last_commit: 93f1afe |
| git_last_commit_date: 2025-11-18 19:53:51 -0500 (Tue, 18 Nov 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-20 11:39 -0500 (Thu, 20 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4827 |
| lconway | macOS 12.7.6 Monterey | x86_64 | R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" | 4600 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4564 |
| 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 2040/2325 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SparseArray 1.11.2 (landing page) Hervé Pagès
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | ERROR | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | ERROR | ERROR | skipped | skipped | |||||||||
|
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: 1.11.2 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SparseArray |
| StartedAt: 2025-11-19 15:22:47 -0500 (Wed, 19 Nov 2025) |
| EndedAt: 2025-11-19 15:23:05 -0500 (Wed, 19 Nov 2025) |
| EllapsedTime: 18.2 seconds |
| RetCode: 1 |
| Status: ERROR |
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###
### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SparseArray
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library’
* installing *source* package ‘SparseArray’ ...
** this is package ‘SparseArray’ version ‘1.11.2’
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using SDK: ‘MacOSX11.3.1.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ExtendableJaggedArray.c -o ExtendableJaggedArray.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c OPBufTree.c -o OPBufTree.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_SparseArray.c -o R_init_SparseArray.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Rvector_summarization.c -o Rvector_summarization.o
Rvector_summarization.c:1360:12: warning: unused function 'any_NA_list_elt' [-Wunused-function]
static int any_NA_list_elt(SEXP x)
^
Rvector_summarization.c:1370:12: warning: unused function 'count_NA_list_elts' [-Wunused-function]
static int count_NA_list_elts(SEXP x)
^
2 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Rvector_utils.c -o Rvector_utils.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SBT_utils.c -o SBT_utils.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SVT_SparseArray_class.c -o SVT_SparseArray_class.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseArray_Arith_methods.c -o SparseArray_Arith_methods.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseArray_Compare_methods.c -o SparseArray_Compare_methods.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseArray_Complex_methods.c -o SparseArray_Complex_methods.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseArray_Logic_methods.c -o SparseArray_Logic_methods.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseArray_Math_methods.c -o SparseArray_Math_methods.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseArray_abind.c -o SparseArray_abind.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseArray_aperm.c -o SparseArray_aperm.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseArray_dim_tuning.c -o SparseArray_dim_tuning.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseArray_matrixStats.c -o SparseArray_matrixStats.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseArray_misc_methods.c -o SparseArray_misc_methods.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseArray_subassignment.c -o SparseArray_subassignment.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseArray_subsetting.c -o SparseArray_subsetting.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseArray_summarization.c -o SparseArray_summarization.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseMatrix_mult.c -o SparseMatrix_mult.o
SparseMatrix_mult.c:306:13: warning: unused function 'crossprod2_doubleSV_doublemat' [-Wunused-function]
static void crossprod2_doubleSV_doublemat(
^
SparseMatrix_mult.c:346:13: warning: unused function 'crossprod2_doublemat_doubleSV' [-Wunused-function]
static void crossprod2_doublemat_doubleSV(
^
2 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseVec.c -o SparseVec.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseVec_Arith.c -o SparseVec_Arith.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseVec_Compare.c -o SparseVec_Compare.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseVec_Logic.c -o SparseVec_Logic.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseVec_Math.c -o SparseVec_Math.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseVec_dotprod.c -o SparseVec_dotprod.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseVec_subassignment.c -o SparseVec_subassignment.o
SparseVec_subassignment.c:63:1: error: expected expression
DEFINE_next_subassign_typeSV_out_val_FUN(int)
^
SparseVec_subassignment.c:55:3: note: expanded from macro 'DEFINE_next_subassign_typeSV_out_val_FUN'
int i = selection2 == NULL ? *k : selection2[*k]; \
^
SparseVec_subassignment.c:63:1: error: use of undeclared identifier 'i'
SparseVec_subassignment.c:56:20: note: expanded from macro 'DEFINE_next_subassign_typeSV_out_val_FUN'
*out_val = vals2[i]; \
^
SparseVec_subassignment.c:64:1: error: expected expression
DEFINE_next_subassign_typeSV_out_val_FUN(double)
^
SparseVec_subassignment.c:55:3: note: expanded from macro 'DEFINE_next_subassign_typeSV_out_val_FUN'
int i = selection2 == NULL ? *k : selection2[*k]; \
^
SparseVec_subassignment.c:64:1: error: use of undeclared identifier 'i'
SparseVec_subassignment.c:56:20: note: expanded from macro 'DEFINE_next_subassign_typeSV_out_val_FUN'
*out_val = vals2[i]; \
^
SparseVec_subassignment.c:65:1: error: expected expression
DEFINE_next_subassign_typeSV_out_val_FUN(Rcomplex)
^
SparseVec_subassignment.c:55:3: note: expanded from macro 'DEFINE_next_subassign_typeSV_out_val_FUN'
int i = selection2 == NULL ? *k : selection2[*k]; \
^
SparseVec_subassignment.c:65:1: error: use of undeclared identifier 'i'
SparseVec_subassignment.c:56:20: note: expanded from macro 'DEFINE_next_subassign_typeSV_out_val_FUN'
*out_val = vals2[i]; \
^
SparseVec_subassignment.c:66:1: error: expected expression
DEFINE_next_subassign_typeSV_out_val_FUN(Rbyte)
^
SparseVec_subassignment.c:55:3: note: expanded from macro 'DEFINE_next_subassign_typeSV_out_val_FUN'
int i = selection2 == NULL ? *k : selection2[*k]; \
^
SparseVec_subassignment.c:66:1: error: use of undeclared identifier 'i'
SparseVec_subassignment.c:56:20: note: expanded from macro 'DEFINE_next_subassign_typeSV_out_val_FUN'
*out_val = vals2[i]; \
^
8 errors generated.
make: *** [SparseVec_subassignment.o] Error 1
ERROR: compilation failed for package ‘SparseArray’
* removing ‘/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/SparseArray’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/SparseArray’