Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘IsoBayes/DESCRIPTION’ ... OK
* preparing ‘IsoBayes’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to process help pages
* saving partial Rd database
* 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 ‘IsoBayes_0.99.2.tar.gz’

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 BiocCheckGitClone('IsoBayes')

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─ BiocCheckVersion: 1.37.7
─ BiocVersion: 3.18
─ Package: IsoBayes
─ PackageVersion: 0.99.2
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3084/IsoBayes_20230807135708/IsoBayes
─ platform: unix
─ isTarBall: FALSE

* Checking valid files...
    * ERROR: System files found that should not be Git tracked.
      src/MCMC_PEP.o
      src/MCMC.o
      src/RcppExports.o
* 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...

─ BiocCheck results ──
1 ERRORS | 0 WARNINGS | 0 NOTES

For more details, run
    browseVignettes(package = 'BiocCheck')




===============================

 R CMD CHECK

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* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/3084/IsoBayes_20230807135708/IsoBayes.Rcheck’
* using R version 4.3.1 Patched (2023-06-17 r84564)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IsoBayes/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IsoBayes’ version ‘0.99.2’
* 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 ‘IsoBayes’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] 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 ... [4s/5s] NOTE
MCMC: no visible binding for global variable ‘_IsoBayes_MCMC’
MCMC_PEP: no visible binding for global variable ‘_IsoBayes_MCMC_PEP’
MCMC_Unique: no visible binding for global variable
  ‘_IsoBayes_MCMC_Unique’
Undefined global functions or variables:
  _IsoBayes_MCMC _IsoBayes_MCMC_PEP _IsoBayes_MCMC_Unique
* checking Rd files ... [0s/0s] 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 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 use of SHLIB_OPENMP_*FLAGS 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 ‘IsoBayes/libs/IsoBayes.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 files in ‘vignettes’ ... OK
* checking examples ... [4s/4s] ERROR
Running examples in ‘IsoBayes-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: inference
> ### Title: Run our two-layer latent variable Bayesian model
> ### Aliases: inference
> 
> ### ** Examples
> 
> # Load internal data to the package:
> data_dir = system.file("extdata", package = "IsoBayes")
> 
> # Define the path to the AllPeptides.psmtsv file returned by MetaMorpheus tool
> path_to_peptides_psm = paste0(data_dir, "/AllPeptides.psmtsv")
> 
> # Define the path to the jurkat_isoform_kallisto.tsv with mRNA relative abundance
> tpm_path = paste0(data_dir, "/jurkat_isoform_kallisto.tsv")
> 
> # Load the data
> data_loaded = load_data(
+   path_to_peptides_psm = path_to_peptides_psm,
+   path_to_tpm = tpm_path)
We found:
10647 protein isoforms.
After FDR filtering (if used), we will analyze:
7521 protein isoforms.
Percentage of unique peptides: 46.26%
> 
> # Define the path to the map_iso_gene.csv file
> path_to_map_iso_gene = paste0(data_dir, "/map_iso_gene.csv")
> 
> # Run the algorithm
> set.seed(169612)
> results = inference(data_loaded, map_iso_gene = path_to_map_iso_gene)
Error in MCMC_PEP(pept_df$EC_numeric, pept_df$Y, pept_df$PEP, M, pept_unique_df$EC_numeric,  : 
  object '_IsoBayes_MCMC_PEP' not found
Calls: inference -> do.call -> run_MCMC_pep -> MCMC_PEP
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [10s/10s]
 [10s/10s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
      pept_unique_df$Y, pept_unique_df$PEP, M_unique, protein_length, 
      pp, N, params$K, params$burn_in, params$thin)`: object '_IsoBayes_MCMC_PEP' not found
  Backtrace:
      ▆
   1. └─IsoBayes::inference(data_loaded, map_iso_gene = path_to_map_iso_gene) at test_inference.R:21:2
   2.   ├─base::do.call("run_MCMC_pep", args_MCMC)
   3.   └─IsoBayes:::run_MCMC_pep(...)
   4.     └─IsoBayes:::MCMC_PEP(...)
  ── Error ('test_plot_relative_abundances.R:21:3'): plot_relative_abundances() works faultlessly. ──
  Error in `MCMC_PEP(pept_df$EC_numeric, pept_df$Y, pept_df$PEP, M, pept_unique_df$EC_numeric, 
      pept_unique_df$Y, pept_unique_df$PEP, M_unique, protein_length, 
      pp, N, params$K, params$burn_in, params$thin)`: object '_IsoBayes_MCMC_PEP' not found
  Backtrace:
      ▆
   1. └─IsoBayes::inference(data_loaded, map_iso_gene = path_to_map_iso_gene) at test_plot_relative_abundances.R:21:2
   2.   ├─base::do.call("run_MCMC_pep", args_MCMC)
   3.   └─IsoBayes:::run_MCMC_pep(...)
   4.     └─IsoBayes:::MCMC_PEP(...)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 2 ]
  Error: Test failures
  Execution halted
* 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 ... [4s/4s] OK
* DONE

Status: 2 ERRORs, 4 NOTEs
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/3084/IsoBayes_20230807135708/IsoBayes.Rcheck/00check.log’
for details.





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 BiocCheck('IsoBayes_0.99.2.tar.gz')

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─ BiocCheckVersion: 1.37.7
─ BiocVersion: 3.18
─ Package: IsoBayes
─ PackageVersion: 0.99.2
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmp3KKlgH/fileba11583f8aed/IsoBayes
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmp3KKlgH/fileba1177051f59
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3084/IsoBayes_20230807135708/IsoBayes.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...
* Checking for pinned package versions...
* 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 IsoBayes...
* Checking coding practice...
    * NOTE: Avoid using '=' for assignment and use '<-' instead
    * NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 4 functions greater than 50 lines.
* 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...
Warning in .rmYAMLfm(lines) :
  More than 2 YAML front matter delimiters, i.e., '---' found
    * NOTE: Consider shorter lines; 245 lines (14%) are > 80 characters
      long.
    * NOTE: Consider 4 spaces instead of tabs; 17 lines (1%) contain
      tabs.
    * NOTE: Consider multiples of 4 spaces for line indents; 570 lines
      (33%) 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...
    * ERROR: Maintainer must subscribe to the bioc-devel mailing list.
      Subscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
    * ERROR: Maintainer must register at the support site; visit
      https://support.bioconductor.org/accounts/signup/

─ BiocCheck results ──
2 ERRORS | 0 WARNINGS | 6 NOTES

See the IsoBayes.BiocCheck folder and run
    browseVignettes(package = 'BiocCheck')
for details.

===============================

 R CMD BUILD

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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir IsoBayes_0.99.2.tar.gz'
>>>>>>> 

* installing *source* package ‘IsoBayes’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c MCMC.cpp -o MCMC.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c MCMC_PEP.cpp -o MCMC_PEP.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c MCMC_Unique.cpp -o MCMC_Unique.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/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++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o IsoBayes.so MCMC.o MCMC_PEP.o MCMC_Unique.o RcppExports.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/pkgbuild/packagebuilder/workers/jobs/3084/IsoBayes_20230807135708/libdir/00LOCK-IsoBayes/00new/IsoBayes/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 (IsoBayes)


>>>>>>> 
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR libdir/IsoBayes/libs/IsoBayes.so
>>>>>>> 

>>>>>>> Paths before fix:
libdir/IsoBayes/libs/IsoBayes.so:
	IsoBayes.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib (compatibility version 4.3.0, current version 4.3.1)
	/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0)
	/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
	/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1)
	/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/4.3-x86_64/Resources/lib/libgcc_s.1.1.dylib" "libdir/IsoBayes/libs/IsoBayes.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libgfortran.5.dylib" "libdir/IsoBayes/libs/IsoBayes.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libquadmath.0.dylib" "libdir/IsoBayes/libs/IsoBayes.so"
install_name_tool -change "/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libgfortran.5.dylib" "libdir/IsoBayes/libs/IsoBayes.so"
install_name_tool -change "/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libquadmath.0.dylib" "libdir/IsoBayes/libs/IsoBayes.so"

>>>>>>> Paths after fix:

libdir/IsoBayes/libs/IsoBayes.so:
	IsoBayes.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib (compatibility version 4.3.0, current version 4.3.1)
	/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1)
	/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)