Wei Shi
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/Rsubread |
| git_branch: devel |
| git_last_commit: e5b2321 |
| git_last_commit_date: 2024-03-26 22:20:56 -0400 (Tue, 26 Mar 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:39:57 -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 1806/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Rsubread 2.17.4 (landing page) Wei Shi
| 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 Rsubread package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rsubread.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: Rsubread |
| Version: 2.17.4 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Rsubread |
| StartedAt: 2024-03-27 15:09:10 -0400 (Wed, 27 Mar 2024) |
| EndedAt: 2024-03-27 15:09:43 -0400 (Wed, 27 Mar 2024) |
| EllapsedTime: 33.1 seconds |
| RetCode: 0 |
| Status: OK |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Rsubread
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘Rsubread’ ...
** using staged installation
@@@@@ The operating system is Darwin.
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c HelperFunctions.c -o HelperFunctions.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c LRMbase-index.c -o LRMbase-index.o
LRMbase-index.c:146:40: warning: variable 'all_mismatched' set but not used [-Wunused-but-set-variable]
int read_chrsor = 0, all_matched = 0, all_mismatched = 0;
^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c LRMchro-event.c -o LRMchro-event.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c LRMfile-io.c -o LRMfile-io.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c LRMhashtable.c -o LRMhashtable.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c LRMhelper.c -o LRMhelper.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c LRMseek-zlib.c -o LRMseek-zlib.o
LRMseek-zlib.c:194:15: warning: variable 'this_chunk_size' set but not used [-Wunused-but-set-variable]
unsigned int this_chunk_size = 0;
^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c R_wrapper.c -o R_wrapper.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c RsimReads.c -o RsimReads.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c SNPCalling.c -o SNPCalling.o
SNPCalling.c:707:7: warning: variable 'window_no' set but not used [-Wunused-but-set-variable]
int window_no = 0;
^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c aligner.c -o aligner.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c atgcContent.c -o atgcContent.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c build-sam-index.c -o build-sam-index.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c cell-counts.c -o cell-counts.o
cell-counts.c:4636:11: warning: variable 'frret' set but not used [-Wunused-but-set-variable]
size_t frret = fread(§ion1_items,1, 8, input_fps[xk1]);
^
cell-counts.c:4661:11: warning: variable 'frret' set but not used [-Wunused-but-set-variable]
size_t frret = fread(last_rbin_buffer[xk1]+16, 1, 8*genes+ cct_context -> UMI_length + 4, input_fps[xk1]);
^
cell-counts.c:4735:11: warning: variable 'frret' set but not used [-Wunused-but-set-variable]
size_t frret = fread(last_rbin_buffer[selected_fp_no]+16, 1, 8*genes+ cct_context -> UMI_length + 4, input_fps[selected_fp_no]);
^
cell-counts.c:4782:10: warning: variable 'frret' set but not used [-Wunused-but-set-variable]
size_t frret = fread(&binlen, 1, 4, notmapped_fp);
^
cell-counts.c:4574:11: warning: variable 'removed_umis' set but not used [-Wunused-but-set-variable]
srInt_64 removed_umis = 0;
^
5 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c core-bigtable.c -o core-bigtable.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c core-indel.c -o core-indel.o
core-indel.c:2592:8: warning: variable 'all_reads' set but not used [-Wunused-but-set-variable]
int all_reads = 0;
^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c core-interface-aligner.c -o core-interface-aligner.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c core-interface-subjunc.c -o core-interface-subjunc.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c core-junction.c -o core-junction.o
core-junction.c:3166:6: warning: variable 'total_perfect_matched_sections' set but not used [-Wunused-but-set-variable]
int total_perfect_matched_sections = 0;
^
core-junction.c:4764:8: warning: variable 'coverage_len' set but not used [-Wunused-but-set-variable]
int coverage_len = max_end - max_start + vote->coverage_end[i][j] - vote->coverage_start[i][j];
^
core-junction.c:5728:13: warning: variable 'small_dist' set but not used [-Wunused-but-set-variable]
long long small_dist = event_body -> event_small_side, large_dist = event_body -> event_large_side;
^
core-junction.c:5728:58: warning: variable 'large_dist' set but not used [-Wunused-but-set-variable]
long long small_dist = event_body -> event_small_side, large_dist = event_body -> event_large_side;
^
4 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c core.c -o core.o
core.c:1373:15: warning: variable 'linear_cursor' set but not used [-Wunused-but-set-variable]
unsigned int linear_cursor = linear;
^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c detection-calls.c -o detection-calls.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c detectionCall.c -o detectionCall.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c detectionCallAnnotation.c -o detectionCallAnnotation.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c exon-algorithms.c -o exon-algorithms.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c exon-align-indel.c -o exon-align-indel.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c exon-align.c -o exon-align.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c flattenAnnotations.c -o flattenAnnotations.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c fullscan.c -o fullscan.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c fusion-align.c -o fusion-align.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c gen_rand_reads.c -o gen_rand_reads.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c gene-algorithms.c -o gene-algorithms.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c gene-value-index.c -o gene-value-index.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c hashtable.c -o hashtable.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c index-builder.c -o index-builder.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c input-blc.c -o input-blc.o
input-blc.c:580:17: warning: unused variable 'npos' [-Wunused-variable]
long long npos = lseek(tfp -> cbcl_bin_fd, next_tile_start_off , SEEK_SET);
^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c input-files.c -o input-files.o
input-files.c:2668:11: warning: variable 'all_orphants' set but not used [-Wunused-but-set-variable]
srInt_64 all_orphants = 0;
^
input-files.c:3242:6: warning: unused variable 'seq_len' [-Wunused-variable]
int seq_len = qual - seq - 1;
^
input-files.c:5262:16: warning: variable 'bam_signature' set but not used [-Wunused-but-set-variable]
unsigned int bam_signature;
^
3 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c interval_merge.c -o interval_merge.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c long-hashtable.c -o long-hashtable.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c longread-mapping.c -o longread-mapping.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c mergeVCF.c -o mergeVCF.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c processExons.c -o processExons.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c propmapped.c -o propmapped.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c qualityScores.c -o qualityScores.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c read-repair.c -o read-repair.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c readSummary.c -o readSummary.o
readSummary.c:3804:16: warning: variable 'assignment_target_number' set but not used [-Wunused-but-set-variable]
srInt_64 assignment_target_number = tmp_voter_id;
^
readSummary.c:3874:25: warning: unused variable 'sample_i' [-Wunused-variable]
int xk1, xk2, ret = 0, sample_i;
^
readSummary.c:5635:45: warning: variable 'scrna_total_BAM_no' set but not used [-Wunused-but-set-variable]
int isGTF, n_input_files=0,is_dual_index, scrna_total_BAM_no;
^
3 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c removeDupReads.c -o removeDupReads.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c sam2bed.c -o sam2bed.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c sambam-file.c -o sambam-file.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c seek-zlib.c -o seek-zlib.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c sorted-hashtable.c -o sorted-hashtable.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c sublog.c -o sublog.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.17.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c tx-unique.c -o tx-unique.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o Rsubread.so HelperFunctions.o LRMbase-index.o LRMchro-event.o LRMfile-io.o LRMhashtable.o LRMhelper.o LRMseek-zlib.o LRMsorted-hashtable.o R_wrapper.o RsimReads.o SNPCalling.o aligner.o atgcContent.o build-sam-index.o cell-counts.o core-bigtable.o core-indel.o core-interface-aligner.o core-interface-subjunc.o core-junction.o core.o detection-calls.o detectionCall.o detectionCallAnnotation.o exon-algorithms.o exon-align-indel.o exon-align.o flattenAnnotations.o fullscan.o fusion-align.o gen_rand_reads.o gene-algorithms.o gene-value-index.o hashtable.o index-builder.o input-blc.o input-files.o interval_merge.o long-hashtable.o longread-mapping.o mergeVCF.o processExons.o propmapped.o qualityScores.o read-repair.o readSummary.o removeDupReads.o sam2bed.o sambam-file.o seek-zlib.o sorted-hashtable.o sublog.o tx-unique.o -lpthread -DMAKE_FOR_EXON -D MACOS -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-Rsubread/00new/Rsubread/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 (Rsubread)