===============================
R CMD BUILD
===============================
* checking for file ‘Rhisat/DESCRIPTION’ ... OK
* preparing ‘Rhisat’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘Rhisat_0.99.15.tar.gz’
===============================
BiocCheckGitClone('Rhisat')
===============================
This is BiocCheckGitClone version 1.31.36. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 0
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2426/c54fee63c1524e2fc1a749dd3ea5c4cb16d1eb0b/Rhisat.Rcheck’
* using R Under development (unstable) (2022-03-02 r81842)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rhisat/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rhisat’ version ‘0.99.15’
* package encoding: UTF-8
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Rhisat’ can be installed ... [393s/404s] OK
* checking installed package size ... NOTE
installed size is 5.3Mb
* checking package directory ... OK
* checking for future file timestamps ... 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 loading without being on the library search path ... OK
* checking use of S3 registration ... 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 ... [5s/5s] OK
* checking Rd files ... [1s/1s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘Rhisat/libs/Rhisat.so’:
Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
It is good practice to register native routines and to disable symbol
search.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [3s/5s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [3s/3s]
[4s/4s] OK
* 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: 4 NOTEs
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2426/c54fee63c1524e2fc1a749dd3ea5c4cb16d1eb0b/Rhisat.Rcheck/00check.log’
for details.
===============================
BiocCheck('Rhisat_0.99.15.tar.gz')
===============================
This is BiocCheck version 1.31.36. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
Warning in system2(cmd, args, stdout = TRUE, stderr = FALSE, env = "R_DEFAULT_PACKAGES=NULL") :
running command 'R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' -q --vanilla --slave -f /Library/Frameworks/R.framework/Versions/4.2/Resources/library/BiocCheck/script/checkBadDeps.R --args "/Users/pkgbuild/packagebuilder/workers/jobs/2426/c54fee63c1524e2fc1a749dd3ea5c4cb16d1eb0b/Rhisat_0.99.15.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//Rtmp4D0GbU/file5b8a2f618225/lib" 2>/dev/null' had status 1
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R Version dependency...
* NOTE: Update R version dependency from 3.5 to 4.2.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* NOTE: License 'GPL (>= 3)' unknown; licenses cannot restrict use
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of Rhisat...
* Checking coding practice...
* NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
R/checkUtils.R (line 63, column 12)
R/hisat.R (line 86, column 11)
* NOTE: Avoid the use of 'paste' in condition signals
Found in files:
R/checkUtils.R (line 23, column 33)
R/checkUtils.R (line 27, column 30)
R/checkUtils.R (line 32, column 26)
R/checkUtils.R (line 50, column 26)
R/hisat.R (line 75, column 18)
* NOTE: Avoid system() ; use system2()
Found in files:
src/hisat/scripts/infer_fraglen.pl (line 92)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* Checking man page documentation...
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 2 lines (0%) are > 80 characters
long.
First 2 lines:
R/checkUtils.R:51 "argument. Please set...
R/hisat.R:62 hisat <- function(bt2Index,samOutput,seq1,...,seq2=NULL,ov...
* NOTE: Consider multiples of 4 spaces for line indents, 22
lines(3%) are not.
First 6 lines:
R/checkUtils.R:6 argname,filePath[i]))
R/checkUtils.R:15 argname,filePath))
R/checkUtils.R:24 "It will be ov...
R/checkUtils.R:25 argname,filePa...
R/checkUtils.R:29 argname,filePath));
R/checkUtils.R:34 argname,filePath));
See http://bioconductor.org/developers/how-to/coding-style/
See styler package: https://cran.r-project.org/package=styler as
described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 7
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir Rhisat_0.99.15.tar.gz'
>>>>>>>
* installing *source* package ‘Rhisat’ ...
** using staged installation
(cd hisat && (make clean -f Makefile))
rm -f hisat-build-s hisat-build-l hisat-align-s hisat-align-l hisat-inspect-s hisat-inspect-l hisat-build-s-debug hisat-build-l-debug hisat-align-s-debug hisat-align-l-debug hisat-inspect-s-debug hisat-inspect-l-debug \
hisat-build-s.exe hisat-build-l.exe hisat-align-s.exe hisat-align-l.exe hisat-inspect-s.exe hisat-inspect-l.exe hisat-build-s-debug.exe hisat-build-l-debug.exe hisat-align-s-debug.exe hisat-align-l-debug.exe hisat-inspect-s-debug.exe hisat-inspect-l-debug.exe \
hisat-src.zip hisat-bin.zip
rm -f core.* .tmp.head
rm -rf *.dSYM
rm -f ../../inst/hisat-align-s
rm -f ../../inst/hisat-build-s
rm -f ../../inst/hisat-align-l
rm -f ../../inst/hisat-build-l
rm -f ../../inst/hisat-inspect-s
rm -f ../../inst/hisat-inspect-l
rm -f ../../inst/hisat
rm -f ../../inst/hisat-build
rm -f ../../inst/hisat-inspect
rm -f hisat-align-s
rm -f hisat-build-s
rm -f hisat-align-l
rm -f hisat-build-l
rm -f hisat-inspect-s
rm -f hisat-inspect-l
rm -f *.so
rm -f *.o
** libs
** arch -
mkdir -p ../inst
(cd hisat && (make CXX="clang++ -mmacosx-version-min=10.13 -std=gnu++14" -f Makefile))
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -O3 -m64 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY \
-fno-strict-aliasing -DHISAT_VERSION="\"`cat HISAT_VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`clang++ -mmacosx-version-min=10.13 -std=gnu++14 -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall \
-I third_party \
-o hisat-build-s hisat_build.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp hisat_build_main.cpp \
-lpthread
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -O3 -m64 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY \
-fno-strict-aliasing -DHISAT_VERSION="\"`cat HISAT_VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`clang++ -mmacosx-version-min=10.13 -std=gnu++14 -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \
-I third_party \
-o hisat-build-l hisat_build.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp hisat_build_main.cpp \
-lpthread
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -O3 -m64 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY \
-fno-strict-aliasing -DHISAT_VERSION="\"`cat HISAT_VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`clang++ -mmacosx-version-min=10.13 -std=gnu++14 -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall \
-I third_party \
-o hisat-align-s hisat.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp sam.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp splice_site.cpp hisat_main.cpp \
-lpthread
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -O3 -m64 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY \
-fno-strict-aliasing -DHISAT_VERSION="\"`cat HISAT_VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`clang++ -mmacosx-version-min=10.13 -std=gnu++14 -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \
-I third_party \
-o hisat-align-l hisat.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp sam.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp splice_site.cpp hisat_main.cpp \
-lpthread
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -O3 -m64 -msse2 -funroll-loops -g3 \
-DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY \
-fno-strict-aliasing -DHISAT_VERSION="\"`cat HISAT_VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`clang++ -mmacosx-version-min=10.13 -std=gnu++14 -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DHISAT_INSPECT_MAIN -Wall \
-I third_party -I . \
-o hisat-inspect-s hisat_inspect.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \
-lpthread
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -O3 -m64 -msse2 -funroll-loops -g3 \
-DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY \
-fno-strict-aliasing -DHISAT_VERSION="\"`cat HISAT_VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`clang++ -mmacosx-version-min=10.13 -std=gnu++14 -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DHISAT_INSPECT_MAIN -Wall \
-I third_party -I . \
-o hisat-inspect-l hisat_inspect.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \
-lpthread
(cd hisat && (make move -f Makefile))
mv hisat-build-s ../../inst
mv hisat-align-s ../../inst
mv hisat-build-l ../../inst
mv hisat-align-l ../../inst
mv hisat-inspect-s ../../inst
mv hisat-inspect-l ../../inst
cp hisat ../../inst
cp hisat-build ../../inst
cp hisat-inspect ../../inst
(cd hisat && (make clean_dSYM -f Makefile))
rm -rf *.dSYM
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -shared -fPIC -o Rhisat.so version_info.cpp
installing to /Users/pkgbuild/packagebuilder/workers/jobs/2426/c54fee63c1524e2fc1a749dd3ea5c4cb16d1eb0b/libdir/00LOCK-Rhisat/00new/Rhisat/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 (Rhisat)
>>>>>>>
>>>>>>> FIXING LINKS FOR libdir/Rhisat/libs/Rhisat.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgcc_s.1.dylib" "libdir/Rhisat/libs/Rhisat.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgfortran.5.dylib" "libdir/Rhisat/libs/Rhisat.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libquadmath.0.dylib" "libdir/Rhisat/libs/Rhisat.so"