Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘bandle/DESCRIPTION’ ... OK
* preparing ‘bandle’:
* 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 ‘bandle_0.99.1.tar.gz’

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 BiocCheckGitClone('bandle')

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This is BiocCheckGitClone version 1.31.34. 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...


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




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 R CMD CHECK

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* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2521/df2b275ae5706c77df83366537af7c09a5398894/bandle.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bandle/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘bandle’ version ‘0.99.1’
* 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 ‘bandle’ can be installed ... [163s/198s] WARNING
Found the following significant warnings:
  Bessel2ndKind.cpp:798:59: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Bessel2ndKind.cpp:993:53: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Users/pkgbuild/packagebuilder/workers/jobs/2521/df2b275ae5706c77df83366537af7c09a5398894/bandle.Rcheck/00install.out’ for details.
* 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 ... 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 ... NOTE
'library' or 'require' call to ‘Biobase’ which was already attached by Depends.
  Please remove these calls from your code.
':::' call which should be '::': ‘dplyr:::summarise’
  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 ... [77s/91s] 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 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 ... WARNING
File ‘bandle/libs/bandle.so’:
  Found ‘___assert_rtn’, possibly from ‘assert’ (C)
    Object: ‘Bessel2ndKind.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [109s/109s] OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
bandle       63.533  1.398  64.951
bandle-gpfit 15.152  0.307  15.460
bandle-plots  9.108  0.420   9.530
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ ERROR
TIMEOUT: R CMD check exceeded 14 mins






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 BiocCheck('bandle_0.99.1.tar.gz')

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This is BiocCheck version 1.31.34. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
 [120s/120s]
 [120s/120s] 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: 2 WARNINGs, 1 NOTE
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/2521/df2b275ae5706c77df83366537af7c09a5398894/bandle.Rcheck/00check.log’
for details.


* 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/2521/df2b275ae5706c77df83366537af7c09a5398894/bandle_0.99.1.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpywAmSa/file140246dbabd2f/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 4.1 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...
* 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 bandle...
    * WARNING: Avoid the use of 'library' or 'require' in R code
      Found in files:
        require() in R/bandle-sampler.R (line 105, column 22)
* Checking coding practice...
    * NOTE: Avoid sapply(); use vapply()
      Found in files:
        R/bandle-class.R (line 10, column 36)
        R/bandle-class.R (line 41, column 40)
        R/bandle-class.R (line 149, column 38)
        R/bandle-function.R (line 147, column 31)
        R/bandle-function.R (line 153, column 31)
        R/bandle-function.R (line 159, column 28)
        R/bandle-function.R (line 168, column 21)
        R/bandle-plots.R (line 483, column 5)
        R/bandle-utils.R (line 132, column 14)
    * NOTE: Avoid using '=' for assignment and use '<-' instead
      Found in files:
        R/bandle-function.R (line 366, column 28)
        R/bandle-function.R (line 367, column 28)
        R/bandle-function.R (line 368, column 21)
        R/bandle-plots.R (line 348, column 22)
        R/bandle-plots.R (line 349, column 22)
        R/bandle-plots.R (line 350, column 29)
        R/bandle-plots.R (line 367, column 22)
        R/bandle-plots.R (line 368, column 22)
        R/bandle-plots.R (line 369, column 29)
        R/bandle-sampler.R (line 184, column 42)
        R/bandle-sampler.R (line 186, column 42)
    * WARNING: Remove set.seed usage (found 1 times)
        set.seed() in R/bandle-sampler.R (line 136, column 5)
* Checking parsed R code in R directory, examples, vignettes...
    Found @ in vignettes/v01-getting-started.Rmd
    Found @ in vignettes/v02-workflow.Rmd
    * NOTE: Use accessors; don't access S4 class slots via '@' in
      examples/vignettes.
    * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1
      times)
        suppressMessages() in R/bandle-sampler.R (line 105, column 5)
* Checking function lengths...
    * NOTE: Recommended function length <= 50 lines.
      There are 13 functions > 50 lines.
      The longest 5 functions are:
        diffLoc() (R/bandle-sampler.R, line 80): 436 lines
        plotTranslocations() (R/bandle-plots.R, line 249): 215 lines
        bandle() (R/bandle-function.R, line 88): 154 lines
        bandleProcess() (R/bandle-function.R, line 354): 152 lines
        sim_dynamic() (R/simDynamic.R, line 33): 123 lines
* Checking man page documentation...
    * NOTE: Consider adding runnable examples to the following man
      pages which document exported objects:
      bandleParams.Rd
* 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; 458 lines (6%) are > 80 characters
      long.
    First 6 lines:
      R/bandle-class.R:11                                           function(...
      R/bandle-class.R:13                                 msg <- validMsg(msg...
      R/bandle-class.R:23 ##'     probability in an `bandleSummary` instance ...
      R/bandle-class.R:33 ##' different conditions results in an `bandleSumma...
      R/bandle-class.R:42                                               funct...
      R/bandle-class.R:44                                     msg <- validMsg...
    * NOTE: Consider multiples of 4 spaces for line indents, 1040
      lines(14%) are not.
    First 6 lines:
      R/bandle-class.R:11                                           function(...
      R/bandle-class.R:27                          slots = c(posteriorEstimat...
      R/bandle-class.R:28                                    diagnostics = "m...
      R/bandle-class.R:29                                    bandle.joint = "...
      R/bandle-class.R:42                                               funct...
      R/bandle-class.R:74                           slots = c(method = "chara...
    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...
    * 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...
    Maintainer is registered at support site.
    Package name is in support site watched tags.


Summary:
ERROR count: 1
WARNING count: 2
NOTE count: 9
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
BiocCheck FAILED.

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 R CMD BUILD

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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir bandle_0.99.1.tar.gz'
>>>>>>> 

* installing *source* package ‘bandle’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c Bessel2ndKind.cpp -o Bessel2ndKind.o
Bessel2ndKind.cpp:798:59: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
                                               nk, tau, D = D, j + 1, nu).t();
                                                        ~ ^ ~
Bessel2ndKind.cpp:993:53: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
                                         nk, tau, D = D, j + 1).t();
                                                  ~ ^ ~
2 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c dmvtCpp.cpp -o dmvtCpp.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c leapfrogGPcpp.cpp -o leapfrogGPcpp.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c pg_sample.cpp -o pg_sample.o
clang++ -mmacosx-version-min=10.13 -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/usr/local/lib -o bandle.so Bessel2ndKind.o RcppExports.o dmvtCpp.o leapfrogGPcpp.o pg_sample.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/pkgbuild/packagebuilder/workers/jobs/2521/df2b275ae5706c77df83366537af7c09a5398894/libdir/00LOCK-bandle/00new/bandle/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 (bandle)


>>>>>>> 
>>>>>>> FIXING LINKS FOR libdir/bandle/libs/bandle.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/bandle/libs/bandle.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgfortran.5.dylib" "libdir/bandle/libs/bandle.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libquadmath.0.dylib" "libdir/bandle/libs/bandle.so"
install_name_tool -change "/usr/local/gfortran/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgfortran.5.dylib" "libdir/bandle/libs/bandle.so"
install_name_tool -change "/usr/local/gfortran/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libquadmath.0.dylib" "libdir/bandle/libs/bandle.so"