merida1 Summary
[top]
Package: bandle |
Version: 0.99.0 |
RVersion: 4.2
|
BiocVersion: 3.15
|
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data bandle |
BuildTime: 5 minutes 6.84 seconds |
CheckCommand: BiocCheckGitClone('bandle') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch bandle_0.99.0.tar.gz && BiocCheck('bandle_0.99.0.tar.gz', `new-package`=TRUE) |
CheckTime: 9 minutes 20.36 seconds |
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh bandle_0.99.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
BuildBinTime: 1 minutes 20.00 seconds |
PackageFileSize: 3114.96 KiB |
BuildID:: bandle_20220208144158 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: bandle. Starting Build package. Starting Check package. Starting Build package. |
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 1. Installing package status: 0. Build Package status: 0. Checking Package status: 1. Build Package status: 0. |
merida1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* 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_0.99.0.tar.gz’
merida1 CHECK output
[top]
===============================
BiocCheckGitClone('bandle')
===============================
This is BiocCheckGitClone version 1.31.34. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* ERROR: System Files found that should not be git tracked:
.gitattributes
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
Summary:
ERROR count: 1
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
BiocCheckGitClone FAILED.
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2521/bandle_20220208144158/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 ‘0.99.0’
* 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 ... [94s/94s] 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/bandle_20220208144158/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 ... [39s/39s] OK
* 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 ... 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 ... [99s/99s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
bandle 58.456 1.199 59.698
bandle-gpfit 13.703 0.249 13.970
bandle-plots 8.295 0.355 8.677
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [121s/121s]
[121s/121s] 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/bandle_20220208144158/bandle.Rcheck/00check.log’
for details.
===============================
BiocCheck('bandle_0.99.0.tar.gz')
===============================
This is BiocCheck version 1.31.34. 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/2521/bandle_20220208144158/bandle_0.99.0.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpgR8QO4/file8f036fc1092e/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.
merida1 BUILD BIN output
[top]
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir bandle_0.99.0.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/bandle_20220208144158/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"
nebbiolo1 Summary
[top]
Package: bandle |
Version: 0.99.0 |
RVersion: 4.2
|
BiocVersion: 3.15
|
BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data bandle |
BuildTime: 5 minutes 12.81 seconds |
CheckCommand: BiocCheckGitClone('bandle') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings bandle_0.99.0.tar.gz && BiocCheck('bandle_0.99.0.tar.gz', `new-package`=TRUE) |
CheckTime: 5 minutes 52.51 seconds |
BuildBinCommand: |
BuildBinTime: |
PackageFileSize: 3094.55 KiB |
BuildID:: bandle_20220208144158 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: bandle. Starting Build package. Starting Check package. |
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 1. Installing package status: 0. Build Package status: 0. Checking Package status: 1. |
nebbiolo1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* 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_0.99.0.tar.gz’
nebbiolo1 CHECK output
[top]
===============================
BiocCheckGitClone('bandle')
===============================
This is BiocCheckGitClone version 1.31.34. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* ERROR: System Files found that should not be git tracked:
.gitattributes
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
Summary:
ERROR count: 1
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
BiocCheckGitClone FAILED.
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2521/bandle_20220208144158/bandle.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-pc-linux-gnu (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 ‘0.99.0’
* 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 ... [62s/62s] OK
* checking installed package size ... NOTE
installed size is 7.2Mb
sub-directories of 1Mb or more:
doc 2.3Mb
libs 4.2Mb
* 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 ... [25s/25s] OK
* 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [61s/61s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
bandle 34.922 0.244 35.167
bandle-gpfit 8.028 0.212 8.243
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [73s/73s]
[73s/73s] 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 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2521/bandle_20220208144158/bandle.Rcheck/00check.log’
for details.
===============================
BiocCheck('bandle_0.99.0.tar.gz')
===============================
This is BiocCheck version 1.31.34. 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 '/home/biocbuild/bbs-3.15-bioc/R/bin/R' -q --vanilla --slave -f /home/biocbuild/bbs-3.15-bioc/R/library/BiocCheck/script/checkBadDeps.R --args "/home/pkgbuild/packagebuilder/workers/jobs/2521/bandle_20220208144158/bandle_0.99.0.tar.gz" "/tmp/Rtmp1vWAlD/file3b096d423a15f4/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.
nebbiolo1 BUILD BIN output
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