| Back to Using R 4.1.3 to BUILD/CHECK a small subset of 3.18 packages |
This page was generated on 2024-03-08 16:41:48 -0500 (Fri, 08 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 655 |
| 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 97/118 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||||
| Rsubread 2.16.1 (landing page) Wei Shi
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ||||||||
|
To the developers/maintainers of the Rsubread package: - 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: 2.16.1 |
| Command: /home/hpages/bbs-3.18-bioc-R41/R/bin/R CMD INSTALL Rsubread |
| StartedAt: 2024-03-08 15:28:22 -0500 (Fri, 08 Mar 2024) |
| EndedAt: 2024-03-08 15:29:04 -0500 (Fri, 08 Mar 2024) |
| EllapsedTime: 42.2 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/hpages/bbs-3.18-bioc-R41/R/bin/R CMD INSTALL Rsubread
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* installing to library ‘/home/hpages/bbs-3.18-bioc-R41/R/site-library’
* installing *source* package ‘Rsubread’ ...
** using staged installation
@@@@@ The operating system is Linux.
** libs
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c HelperFunctions.c -o HelperFunctions.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c LRMbase-index.c -o LRMbase-index.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c LRMchro-event.c -o LRMchro-event.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c LRMfile-io.c -o LRMfile-io.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c LRMhashtable.c -o LRMhashtable.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c LRMhelper.c -o LRMhelper.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c LRMseek-zlib.c -o LRMseek-zlib.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c R_wrapper.c -o R_wrapper.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c RsimReads.c -o RsimReads.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c SNPCalling.c -o SNPCalling.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c aligner.c -o aligner.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c atgcContent.c -o atgcContent.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c build-sam-index.c -o build-sam-index.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c cell-counts.c -o cell-counts.o
cell-counts.c: In function ‘cellCounts_find_hits_for_mapped_section’:
cell-counts.c:1611:19: warning: ‘search_start’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1611 | if(search_start>0xffffff00) return;
| ^
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c core-bigtable.c -o core-bigtable.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c core-indel.c -o core-indel.o
core-indel.c: In function ‘rectify_read_text’:
core-indel.c:2846:14: warning: variable ‘changed’ set but not used [-Wunused-but-set-variable]
2846 | char changed[200];
| ^~~~~~~
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c core-interface-aligner.c -o core-interface-aligner.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c core-interface-subjunc.c -o core-interface-subjunc.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c core-junction.c -o core-junction.o
core-junction.c: In function ‘find_donor_receptor’:
core-junction.c:2099:25: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
2099 | if(0&& FIXLENstrcmp("V0112_0155:7:1101:12618:2466#ACTTGA", rname) == 0)
| ^~
core-junction.c:2103:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
2103 | if( (end_site_mismatches + start_site_mismatches) * 500 + insertion_in_between_i < best_testing_score ){
| ^~
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c core.c -o core.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c detection-calls.c -o detection-calls.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c detectionCall.c -o detectionCall.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c detectionCallAnnotation.c -o detectionCallAnnotation.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c exon-algorithms.c -o exon-algorithms.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c exon-align-indel.c -o exon-align-indel.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c exon-align.c -o exon-align.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c flattenAnnotations.c -o flattenAnnotations.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c fullscan.c -o fullscan.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c fusion-align.c -o fusion-align.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c gen_rand_reads.c -o gen_rand_reads.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c gene-algorithms.c -o gene-algorithms.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c gene-value-index.c -o gene-value-index.o
gene-value-index.c: In function ‘is_offset_in_chro’:
gene-value-index.c:85:33: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
85 | if( pos < chros -> padding || pos >= ( chros->read_offsets[n] - chros->read_offsets[n-1] - chros -> padding ))
| ^~
In file included from gene-value-index.h:24,
from gene-value-index.c:25:
subread.h:154:24: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
154 | #define SUBREADprintf msgqu_printf
| ^~~~~~~~~~~~
gene-value-index.c:87:41: note: in expansion of macro ‘SUBREADprintf’
87 | SUBREADprintf("INCHRO:%d ; POS:%d\n", ret, pos);
| ^~~~~~~~~~~~~
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c hashtable.c -o hashtable.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c index-builder.c -o index-builder.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c input-blc.c -o input-blc.o
input-blc.c: In function ‘iCache_continuous_read_lanes’:
input-blc.c:580:59: warning: unused variable ‘npos’ [-Wunused-variable]
580 | long long npos = lseek(tfp -> cbcl_bin_fd, next_tile_start_off , SEEK_SET);
| ^~~~
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c input-files.c -o input-files.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c interval_merge.c -o interval_merge.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c long-hashtable.c -o long-hashtable.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c longread-mapping.c -o longread-mapping.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c mergeVCF.c -o mergeVCF.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c processExons.c -o processExons.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c propmapped.c -o propmapped.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c qualityScores.c -o qualityScores.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c read-repair.c -o read-repair.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c readSummary.c -o readSummary.o
readSummary.c: In function ‘vote_and_add_count’:
readSummary.c:4923:66: warning: ‘longest_overlap_score’ may be used uninitialized in this function [-Wmaybe-uninitialized]
4923 | if(longest_overlap_score > scoring_numbers[score_x1]) scoring_numbers[score_x1] = 0;
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c removeDupReads.c -o removeDupReads.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c sam2bed.c -o sam2bed.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c sambam-file.c -o sambam-file.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c seek-zlib.c -o seek-zlib.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c sorted-hashtable.c -o sorted-hashtable.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c sublog.c -o sublog.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fpic -g -O2 -Wall -c tx-unique.c -o tx-unique.o
gcc -shared -L/home/hpages/bbs-3.18-bioc-R41/R/lib -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 -L/home/hpages/bbs-3.18-bioc-R41/R/lib -lR
installing to /home/hpages/bbs-3.18-bioc-R41/R/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
‘Rsubread.Rnw’
** 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)