nebbiolo1 Summary
[top]
| Package: MIRit |
| Version: 0.99.9 |
| RVersion: 4.4
|
| BiocVersion: 3.19
|
| BuildCommand: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data MIRit |
| BuildTime: 1 minutes 7.67 seconds |
| CheckCommand: BiocCheckGitClone('MIRit') && /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3249/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3249/353dc837b639081c792be97600b3388e318fb8d8/MIRit.install-out.txt MIRit_0.99.9.tar.gz && BiocCheck('MIRit_0.99.9.tar.gz', `new-package`=TRUE) |
| CheckTime: 4 minutes 1.43 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 2836.87 KiB |
| BuildID:: MIRit_20240201121312 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: MIRit. Starting Build package. Starting Check package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.Checking Package status: 0. |
nebbiolo1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file MIRit/DESCRIPTION ... OK
* preparing MIRit:
* 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
* looking to see if a data/datalist file should be added
* building MIRit_0.99.9.tar.gz
nebbiolo1 CHECK output
[top]
===============================
BiocCheckGitClone('MIRit')
===============================
BiocCheckVersion: 1.39.21
BiocVersion: 3.19
Package: MIRit
PackageVersion: 0.99.9
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3249/353dc837b639081c792be97600b3388e318fb8d8/MIRit
platform: unix
isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
BiocCheck results
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3249/353dc837b639081c792be97600b3388e318fb8d8/MIRit.Rcheck
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* using option --no-vignettes
* checking for file MIRit/DESCRIPTION ... OK
* this is package MIRit version 0.99.9
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package MIRit can be installed ... OK
* used C++ compiler: g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* checking installed package size ... OK
* 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 ... [7s/7s] OK
* checking whether the package can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the package can be unloaded cleanly ... [7s/7s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [7s/7s] OK
* checking loading without being on the library search path ... [7s/7s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
'graphite:::convertEdges' 'graphite:::selectDb'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [31s/31s] 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 contents of data directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking line endings in C/C++/Fortran sources/headers ... 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
* checking files in vignettes ... OK
* checking examples ... [41s/41s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [23s/19s]
[23s/19s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [4s/4s] OK
* DONE
Status: 2 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/3249/353dc837b639081c792be97600b3388e318fb8d8/MIRit.Rcheck/00check.log
for details.
===============================
BiocCheck('MIRit_0.99.9.tar.gz')
===============================
BiocCheckVersion: 1.39.21
BiocVersion: 3.19
Package: MIRit
PackageVersion: 0.99.9
sourceDir: /tmp/Rtmp4XP4nG/file120720ae5f368/MIRit
installDir: /tmp/Rtmp4XP4nG/file12072011681411
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3249/353dc837b639081c792be97600b3388e318fb8d8/MIRit.BiocCheck
platform: unix
isTarBall: TRUE
* Installing package...
* 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...
* 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 recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
Bioconductor dependencies found in Imports & Depends (46%).
* Checking for pinned package versions in DESCRIPTION...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of MIRit...
* Checking coding practice...
* NOTE: Avoid the use of 'paste' in condition signals
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 5
times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 45 functions greater than 50 lines.
* Checking man page documentation...
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
* NOTE: Usage of dontrun{} / donttest{} tags found in man page
examples. 17% of man pages use at least one of these tags.
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* NOTE: skip_on_bioc() found in testthat files: test-association.R
test-differential-expression.R test-targets.R
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 165 lines (1%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 19 lines
(0%) are not.
See https://contributions.bioconductor.org/r-code.html
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 is in the Support Site Watched Tags.
BiocCheck results
0 ERRORS | 0 WARNINGS | 9 NOTES
See the MIRit.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo1 BUILD BIN output
[top]
merida1 Summary
[top]
| Package: MIRit |
| Version: 0.99.9 |
| RVersion: 4.4
|
| BiocVersion: 3.19
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data MIRit |
| BuildTime: 3 minutes 26.43 seconds |
| CheckCommand: BiocCheckGitClone('MIRit') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/3249/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/3249/353dc837b639081c792be97600b3388e318fb8d8/MIRit.install-out.txt MIRit_0.99.9.tar.gz && BiocCheck('MIRit_0.99.9.tar.gz', `new-package`=TRUE) |
| CheckTime: 11 minutes 1.92 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh MIRit_0.99.9.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 1 minutes 46.58 seconds |
| PackageFileSize: 3111.37 KiB |
| BuildID:: MIRit_20240201121312 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: MIRit. Starting Build package. Starting Check package. Starting Build package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.WARNING: check time exceeded 10 min. Build Package status: 0. |
merida1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file MIRit/DESCRIPTION ... OK
* preparing MIRit:
* 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
* looking to see if a data/datalist file should be added
* building MIRit_0.99.9.tar.gz
merida1 CHECK output
[top]
===============================
BiocCheckGitClone('MIRit')
===============================
BiocCheckVersion: 1.39.21
BiocVersion: 3.19
Package: MIRit
PackageVersion: 0.99.9
sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3249/353dc837b639081c792be97600b3388e318fb8d8/MIRit
platform: unix
isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
BiocCheck results
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory /Users/pkgbuild/packagebuilder/workers/jobs/3249/353dc837b639081c792be97600b3388e318fb8d8/MIRit.Rcheck
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option --no-vignettes
* checking for file MIRit/DESCRIPTION ... OK
* this is package MIRit version 0.99.9
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package MIRit can be installed ... OK
* used C++ compiler: Apple clang version 14.0.0 (clang-1400.0.29.202)
* used SDK: MacOSX11.3.sdk
* checking installed package size ... OK
* 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 ... [17s/22s] OK
* checking whether the package can be loaded with stated dependencies ... [16s/24s] OK
* checking whether the package can be unloaded cleanly ... [16s/21s] OK
* checking whether the namespace can be loaded with stated dependencies ... [16s/18s] OK
* checking whether the namespace can be unloaded cleanly ... [17s/22s] OK
* checking loading without being on the library search path ... [17s/21s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
'graphite:::convertEdges' 'graphite:::selectDb'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [72s/84s] OK
* checking Rd files ... [2s/2s] 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 contents of data directory ... OK
* checking data for non-ASCII characters ... [1s/1s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking line endings in C/C++/Fortran sources/headers ... 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
* checking files in vignettes ... OK
* checking examples ... [76s/92s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
enrichGenes 5.697 0.300 8.311
mirnaIntegration 4.675 0.548 5.452
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [59s/65s]
[59s/66s] ERROR
Running the tests in tests/testthat.R failed.
Last 20 lines of output:
A statistically significant association between 3 DE-miRNAs and 5 genes was found!
As specified by the user, a fry will be used.
Performing miRNA-gene integrative analysis using 'fry' method...
A statistically significant association between 2 DE-miRNAs and 4 genes was found!
[ FAIL 1 | WARN 0 | SKIP 6 | PASS 31 ]
Skipped tests (6)
On Bioconductor (4): 'test-association.R:13:5',
'test-differential-expression.R:17:5', 'test-targets.R:3:5',
'test-targets.R:21:5'
On CRAN (2): 'test-topological-integration.R:23:5', 'test-utils.R:20:5'
Failed tests
Failure ('test-enrichment.R:47:5'): basic GSEA enrichment works
sum(enrTab$pval) (`actual`) not equal to 2.13306691361402 (`expected`).
`actual`: 2.1326
`expected`: 2.1331
[ FAIL 1 | WARN 0 | SKIP 6 | PASS 31 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [17s/18s] OK
* DONE
Status: 1 ERROR, 2 NOTEs
See
/Users/pkgbuild/packagebuilder/workers/jobs/3249/353dc837b639081c792be97600b3388e318fb8d8/MIRit.Rcheck/00check.log
for details.
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('MIRit_0.99.9.tar.gz')
===============================
BiocCheckVersion: 1.39.21
BiocVersion: 3.19
Package: MIRit
PackageVersion: 0.99.9
sourceDir: /var/folders/97/7zyjn3nj10x926_ht39w_4lm0000gt/T//RtmpeivHUx/filef86e5a17b1f1/MIRit
installDir: /var/folders/97/7zyjn3nj10x926_ht39w_4lm0000gt/T//RtmpeivHUx/filef86e9eedd39
BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3249/353dc837b639081c792be97600b3388e318fb8d8/MIRit.BiocCheck
platform: unix
isTarBall: TRUE
* Installing package...
* 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...
* 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 recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
Bioconductor dependencies found in Imports & Depends (46%).
* Checking for pinned package versions in DESCRIPTION...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of MIRit...
* Checking coding practice...
* NOTE: Avoid the use of 'paste' in condition signals
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 5
times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 45 functions greater than 50 lines.
* Checking man page documentation...
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
* NOTE: Usage of dontrun{} / donttest{} tags found in man page
examples. 17% of man pages use at least one of these tags.
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* NOTE: skip_on_bioc() found in testthat files: test-association.R
test-differential-expression.R test-targets.R
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 165 lines (1%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 19 lines
(0%) are not.
See https://contributions.bioconductor.org/r-code.html
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 is in the Support Site Watched Tags.
BiocCheck results
0 ERRORS | 0 WARNINGS | 9 NOTES
See the MIRit.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
merida1 BUILD BIN output
[top]
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir MIRit_0.99.9.tar.gz'
>>>>>>>
* installing *source* package MIRit ...
** using staged installation
** libs
using C++ compiler: Apple clang version 14.0.0 (clang-1400.0.29.202)
using SDK: MacOSX11.3.sdk
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pathwayScore.cpp -o pathwayScore.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o MIRit.so RcppExports.o pathwayScore.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/pkgbuild/packagebuilder/workers/jobs/3249/353dc837b639081c792be97600b3388e318fb8d8/libdir/00LOCK-MIRit/00new/MIRit/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (MIRit)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR libdir/MIRit/libs/MIRit.so
>>>>>>>
>>>>>>> Paths before fix:
libdir/MIRit/libs/MIRit.so:
MIRit.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgcc_s.1.1.dylib" "libdir/MIRit/libs/MIRit.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgfortran.5.dylib" "libdir/MIRit/libs/MIRit.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libquadmath.0.dylib" "libdir/MIRit/libs/MIRit.so"
>>>>>>> Paths after fix:
libdir/MIRit/libs/MIRit.so:
MIRit.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)