Wei Shi
| Snapshot Date: 2024-03-26 09:00:03 -0400 (Tue, 26 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/Rsubread |
| git_branch: RELEASE_3_18 |
| git_last_commit: b1a6ee9 |
| git_last_commit_date: 2024-01-21 14:54:10 -0400 (Sun, 21 Jan 2024) |
| Back to Mac ARM64 build report for BioC 3.18 |
|
This page was generated on 2024-03-28 11:32:30 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4376 |
| 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 1809/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Rsubread 2.16.1 (landing page) Wei Shi
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | 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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Rsubread.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Rsubread_2.16.1.tar.gz |
| StartedAt: 2024-03-28 01:15:52 -0400 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 01:30:49 -0400 (Thu, 28 Mar 2024) |
| EllapsedTime: 896.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Rsubread.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Rsubread.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Rsubread_2.16.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/Rsubread.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rsubread/DESCRIPTION’ ... OK
* this is package ‘Rsubread’ version ‘2.16.1’
* 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 ‘Rsubread’ can be installed ... OK
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... NOTE
installed size is 36.8Mb
sub-directories of 1Mb or more:
annot 30.9Mb
libs 1.1Mb
qualf 3.4Mb
* 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 R 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 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 shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
align 156.128 231.649 390.827
propmapped 156.205 229.745 389.423
sublong 31.096 5.038 36.432
buildindex 14.744 2.894 17.946
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/Rsubread.Rcheck/00check.log’
for details.
Rsubread.Rcheck/00install.out
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Rsubread
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘Rsubread’ ...
** using staged installation
@@@@@ The operating system is Darwin.
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fPIC -falign-functions=64 -Wall -g -O2 -c HelperFunctions.c -o HelperFunctions.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -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 arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fPIC -falign-functions=64 -Wall -g -O2 -c LRMchro-event.c -o LRMchro-event.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fPIC -falign-functions=64 -Wall -g -O2 -c LRMfile-io.c -o LRMfile-io.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fPIC -falign-functions=64 -Wall -g -O2 -c LRMhashtable.c -o LRMhashtable.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fPIC -falign-functions=64 -Wall -g -O2 -c LRMhelper.c -o LRMhelper.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -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 arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fPIC -falign-functions=64 -Wall -g -O2 -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fPIC -falign-functions=64 -Wall -g -O2 -c R_wrapper.c -o R_wrapper.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fPIC -falign-functions=64 -Wall -g -O2 -c RsimReads.c -o RsimReads.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fPIC -falign-functions=64 -Wall -g -O2 -c SNPCalling.c -o SNPCalling.o
SNPCalling.c:263:25: warning: variable 'OVERLAPPED_BASES' set but not used [-Wunused-but-set-variable]
unsigned long long int OVERLAPPED_BASES=0;
^
SNPCalling.c:264:25: warning: variable 'OVER_MISMA_BASES' set but not used [-Wunused-but-set-variable]
unsigned long long int OVER_MISMA_BASES=0;
^
SNPCalling.c:265:25: warning: variable 'ALL_BASES' set but not used [-Wunused-but-set-variable]
unsigned long long int ALL_BASES=0;
^
SNPCalling.c:707:7: warning: variable 'window_no' set but not used [-Wunused-but-set-variable]
int window_no = 0;
^
4 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fPIC -falign-functions=64 -Wall -g -O2 -c aligner.c -o aligner.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fPIC -falign-functions=64 -Wall -g -O2 -c atgcContent.c -o atgcContent.o
atgcContent.c:72:7: warning: variable 'line_num' set but not used [-Wunused-but-set-variable]
int line_num = 0;
^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fPIC -falign-functions=64 -Wall -g -O2 -c build-sam-index.c -o build-sam-index.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fPIC -falign-functions=64 -Wall -g -O2 -c cell-counts.c -o cell-counts.o
cell-counts.c:4619:11: 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:4644:11: 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:4718:11: 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:4765:10: warning: variable 'frret' set but not used [-Wunused-but-set-variable]
size_t frret = fread(&binlen, 1, 4, notmapped_fp);
^
cell-counts.c:4557:11: warning: variable 'removed_umis' set but not used [-Wunused-but-set-variable]
srInt_64 removed_umis = 0;
^
5 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fPIC -falign-functions=64 -Wall -g -O2 -c core-bigtable.c -o core-bigtable.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fPIC -falign-functions=64 -Wall -g -O2 -c core-indel.c -o core-indel.o
core-indel.c:455:32: warning: variable 'all_junctions' set but not used [-Wunused-but-set-variable]
int to_be_removed_number = 0, all_junctions = 0;
^
core-indel.c:2592:8: warning: variable 'all_reads' set but not used [-Wunused-but-set-variable]
int all_reads = 0;
^
core-indel.c:4028:11: warning: variable 'all_indels_in_window' set but not used [-Wunused-but-set-variable]
int all_indels_in_window = 0;
^
core-indel.c:3673:6: warning: variable 'global_read_no' set but not used [-Wunused-but-set-variable]
int global_read_no = 0;
^
4 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fPIC -falign-functions=64 -Wall -g -O2 -c core-interface-aligner.c -o core-interface-aligner.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fPIC -falign-functions=64 -Wall -g -O2 -c core-interface-subjunc.c -o core-interface-subjunc.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fPIC -falign-functions=64 -Wall -g -O2 -c core-junction.c -o core-junction.o
core-junction.c:3165:6: warning: variable 'total_perfect_matched_sections' set but not used [-Wunused-but-set-variable]
int total_perfect_matched_sections = 0;
^
core-junction.c:4153:6: warning: variable 'no_sup_juncs' set but not used [-Wunused-but-set-variable]
int no_sup_juncs = 0;
^
core-junction.c:4154:6: warning: variable 'all_juncs' set but not used [-Wunused-but-set-variable]
int all_juncs = 0;
^
core-junction.c:4285:6: warning: variable 'no_sup_juncs' set but not used [-Wunused-but-set-variable]
int no_sup_juncs = 0, disk_is_full = 0;
^
core-junction.c:4763:8: 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:5727:13: 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:5727:58: 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;
^
7 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fPIC -falign-functions=64 -Wall -g -O2 -c core.c -o core.o
core.c:184:79: warning: variable 'real_lenwidth' set but not used [-Wunused-but-set-variable]
int is_R_code,x1,content_len = strlen(content), state, txt_len, is_cut = 0, real_lenwidth;
^
core.c:1373:15: warning: variable 'linear_cursor' set but not used [-Wunused-but-set-variable]
unsigned int linear_cursor = linear;
^
2 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fPIC -falign-functions=64 -Wall -g -O2 -c detection-calls.c -o detection-calls.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fPIC -falign-functions=64 -Wall -g -O2 -c detectionCall.c -o detectionCall.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fPIC -falign-functions=64 -Wall -g -O2 -c detectionCallAnnotation.c -o detectionCallAnnotation.o
detectionCallAnnotation.c:154:6: warning: variable 'binnum' set but not used [-Wunused-but-set-variable]
int binnum = 0;
^
detectionCallAnnotation.c:184:6: warning: variable 'linenum' set but not used [-Wunused-but-set-variable]
int linenum;
^
detectionCallAnnotation.c:274:6: warning: variable 'linenum' set but not used [-Wunused-but-set-variable]
int linenum;
^
3 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fPIC -falign-functions=64 -Wall -g -O2 -c exon-algorithms.c -o exon-algorithms.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fPIC -falign-functions=64 -Wall -g -O2 -c exon-align-indel.c -o exon-align-indel.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fPIC -falign-functions=64 -Wall -g -O2 -c exon-align.c -o exon-align.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fPIC -falign-functions=64 -Wall -g -O2 -c flattenAnnotations.c -o flattenAnnotations.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fPIC -falign-functions=64 -Wall -g -O2 -c fullscan.c -o fullscan.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fPIC -falign-functions=64 -Wall -g -O2 -c fusion-align.c -o fusion-align.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fPIC -falign-functions=64 -Wall -g -O2 -c gen_rand_reads.c -o gen_rand_reads.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fPIC -falign-functions=64 -Wall -g -O2 -c gene-algorithms.c -o gene-algorithms.o
gene-algorithms.c:795:6: warning: variable 'dynamic_delta' set but not used [-Wunused-but-set-variable]
int dynamic_delta = 0;
^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fPIC -falign-functions=64 -Wall -g -O2 -c gene-value-index.c -o gene-value-index.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fPIC -falign-functions=64 -Wall -g -O2 -c hashtable.c -o hashtable.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fPIC -falign-functions=64 -Wall -g -O2 -c index-builder.c -o index-builder.o
index-builder.c:149:16: warning: variable 'all_skips' set but not used [-Wunused-but-set-variable]
int skips=0, all_skips = 0;
^
index-builder.c:529:10: warning: variable 'read_len' set but not used [-Wunused-but-set-variable]
int i, read_len = 0;
^
index-builder.c:531:16: warning: variable 'all_skips' set but not used [-Wunused-but-set-variable]
int skips=0, all_skips = 0;
^
index-builder.c:476:23: warning: variable 'read_no' set but not used [-Wunused-but-set-variable]
unsigned int offset, read_no;
^
4 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -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 arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -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:2794:6: warning: variable 'current_blocks' set but not used [-Wunused-but-set-variable]
int current_blocks = 0;
^
input-files.c:4966:49: warning: variable 'block_no' set but not used [-Wunused-but-set-variable]
int seq_len = 0, name_len = 0, cigar_opts = 0, block_no=0;
^
input-files.c:4967:11: warning: variable 'reads' set but not used [-Wunused-but-set-variable]
srInt_64 reads =0;
^
input-files.c:5315:16: warning: variable 'bam_signature' set but not used [-Wunused-but-set-variable]
unsigned int bam_signature;
^
input-files.c:5626:7: warning: variable 'reads' set but not used [-Wunused-but-set-variable]
int reads = 0;
^
input-files.c:5857:12: warning: variable 'finished_second_reads' set but not used [-Wunused-but-set-variable]
srInt_64 finished_second_reads = 0;
^
7 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fPIC -falign-functions=64 -Wall -g -O2 -c interval_merge.c -o interval_merge.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fPIC -falign-functions=64 -Wall -g -O2 -c long-hashtable.c -o long-hashtable.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fPIC -falign-functions=64 -Wall -g -O2 -c longread-mapping.c -o longread-mapping.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fPIC -falign-functions=64 -Wall -g -O2 -c mergeVCF.c -o mergeVCF.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fPIC -falign-functions=64 -Wall -g -O2 -c processExons.c -o processExons.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fPIC -falign-functions=64 -Wall -g -O2 -c propmapped.c -o propmapped.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fPIC -falign-functions=64 -Wall -g -O2 -c qualityScores.c -o qualityScores.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fPIC -falign-functions=64 -Wall -g -O2 -c read-repair.c -o read-repair.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fPIC -falign-functions=64 -Wall -g -O2 -c readSummary.c -o readSummary.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fPIC -falign-functions=64 -Wall -g -O2 -c removeDupReads.c -o removeDupReads.o
removeDupReads.c:71:6: warning: variable 'chromosome_block_no' set but not used [-Wunused-but-set-variable]
int chromosome_block_no = 0;
^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fPIC -falign-functions=64 -Wall -g -O2 -c sam2bed.c -o sam2bed.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fPIC -falign-functions=64 -Wall -g -O2 -c sambam-file.c -o sambam-file.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fPIC -falign-functions=64 -Wall -g -O2 -c seek-zlib.c -o seek-zlib.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fPIC -falign-functions=64 -Wall -g -O2 -c sorted-hashtable.c -o sorted-hashtable.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fPIC -falign-functions=64 -Wall -g -O2 -c sublog.c -o sublog.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.16.1\"" -fPIC -falign-functions=64 -Wall -g -O2 -c tx-unique.c -o tx-unique.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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/4.3-arm64/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)
Rsubread.Rcheck/Rsubread-Ex.timings
| name | user | system | elapsed | |
| align | 156.128 | 231.649 | 390.827 | |
| buildindex | 14.744 | 2.894 | 17.946 | |
| cellCounts | 0 | 0 | 0 | |
| featureCounts | 0.000 | 0.001 | 0.000 | |
| findCommonVariants | 0 | 0 | 0 | |
| getInBuiltAnnotation | 0.403 | 0.019 | 0.424 | |
| promoterRegions | 2.391 | 0.033 | 2.426 | |
| propmapped | 156.205 | 229.745 | 389.423 | |
| qualityScores | 0.042 | 0.004 | 0.049 | |
| simReads | 0 | 0 | 0 | |
| sublong | 31.096 | 5.038 | 36.432 | |