| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-10 10:04:40 -0000 (Wed, 10 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" | 6211 |
| 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 | ||||
|
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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1744/2194 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Rsubread 2.15.1 (landing page) Wei Shi
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | TIMEOUT | skipped | |||||||||
| Package: Rsubread |
| Version: 2.15.1 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL Rsubread |
| StartedAt: 2023-05-08 21:23:39 -0000 (Mon, 08 May 2023) |
| EndedAt: 2023-05-08 21:24:40 -0000 (Mon, 08 May 2023) |
| EllapsedTime: 61.1 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL Rsubread
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library’
* installing *source* package ‘Rsubread’ ...
** using staged installation
@@@@@ The operating system is Linux.
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c HelperFunctions.c -o HelperFunctions.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c LRMbase-index.c -o LRMbase-index.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c LRMchro-event.c -o LRMchro-event.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c LRMfile-io.c -o LRMfile-io.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c LRMhashtable.c -o LRMhashtable.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c LRMhelper.c -o LRMhelper.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c LRMseek-zlib.c -o LRMseek-zlib.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c R_wrapper.c -o R_wrapper.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c RsimReads.c -o RsimReads.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c SNPCalling.c -o SNPCalling.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c aligner.c -o aligner.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c atgcContent.c -o atgcContent.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c build-sam-index.c -o build-sam-index.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c cell-counts.c -o cell-counts.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c core-bigtable.c -o core-bigtable.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c core-indel.c -o core-indel.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c core-interface-aligner.c -o core-interface-aligner.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c core-interface-subjunc.c -o core-interface-subjunc.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c core-junction.c -o core-junction.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c core.c -o core.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c detection-calls.c -o detection-calls.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c detectionCall.c -o detectionCall.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c detectionCallAnnotation.c -o detectionCallAnnotation.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c exon-algorithms.c -o exon-algorithms.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c exon-align-indel.c -o exon-align-indel.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c exon-align.c -o exon-align.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c flattenAnnotations.c -o flattenAnnotations.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c fullscan.c -o fullscan.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c fusion-align.c -o fusion-align.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c gen_rand_reads.c -o gen_rand_reads.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c gene-algorithms.c -o gene-algorithms.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c gene-value-index.c -o gene-value-index.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c hashtable.c -o hashtable.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c index-builder.c -o index-builder.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c input-blc.c -o input-blc.o
input-blc.c: In function ‘iCache_write_supIdx_result’:
input-blc.c:1123:30: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 4 has type ‘long int’ [-Wformat=]
1123 | fprintf(ofp, "%s\t%lld\n", (char*)ky, va-NULL);
| ~~~^
| |
| long long int
| %ld
input-blc.c: In function ‘iCache_continuous_read_lanes’:
input-blc.c:489:49: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
489 | read(tfp -> cbcl_bin_fd,&btmp,1);// bits per call.
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-blc.c:491:49: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
491 | read(tfp -> cbcl_bin_fd,&tfp -> bits_per_bitscore,1);// bits per qscore.
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-blc.c:498:49: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
498 | read(tfp -> cbcl_bin_fd,&btmp,4);// Number of bins
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-blc.c:501:57: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
501 | read(tfp -> cbcl_bin_fd,&fromv,4);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-blc.c:502:57: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
502 | read(tfp -> cbcl_bin_fd,&tov,4);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-blc.c:511:49: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
511 | read(tfp -> cbcl_bin_fd,&btmp,4);// Number of tiles (gzipped blocks) in this file
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-blc.c:515:57: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
515 | read(tfp -> cbcl_bin_fd,&tile_4digit,4);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-blc.c:516:57: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
516 | read(tfp -> cbcl_bin_fd,&reads_in_tile,4);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-blc.c:517:57: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
517 | read(tfp -> cbcl_bin_fd,&data_size,4);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-blc.c:518:57: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
518 | read(tfp -> cbcl_bin_fd,&compressed_size,4);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-blc.c:524:49: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
524 | read(tfp -> cbcl_bin_fd,&btmp,1); // excluding non-FP?
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c input-files.c -o input-files.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c interval_merge.c -o interval_merge.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c long-hashtable.c -o long-hashtable.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c longread-mapping.c -o longread-mapping.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c mergeVCF.c -o mergeVCF.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c processExons.c -o processExons.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c propmapped.c -o propmapped.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c qualityScores.c -o qualityScores.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c read-repair.c -o read-repair.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c readSummary.c -o readSummary.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c removeDupReads.c -o removeDupReads.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c sam2bed.c -o sam2bed.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c sambam-file.c -o sambam-file.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c seek-zlib.c -o seek-zlib.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c sorted-hashtable.c -o sorted-hashtable.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c sublog.c -o sublog.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.15.1\"" -fPIC -g -O2 -c tx-unique.c -o tx-unique.o
gcc -shared -L/usr/local/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 -lz -lpthread -DMAKE_FOR_EXON
installing to /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-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)