merida1 Summary
[top]
| Package: epimutacions |
| Version: 0.99.18 |
| RVersion: 4.2
|
| BiocVersion: 3.15
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data epimutacions |
| BuildTime: 4 minutes 10.06 seconds |
| CheckCommand: BiocCheckGitClone('epimutacions') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch epimutacions_0.99.18.tar.gz && BiocCheck('epimutacions_0.99.18.tar.gz', `new-package`=TRUE) |
| CheckTime: 6 minutes 30.73 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh epimutacions_0.99.18.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 41.57 seconds |
| PackageFileSize: 1645.38 KiB |
| BuildID:: epimutacions_20220112162826 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: epimutacions. 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. Checking Package status: 0. Build Package status: 0. |
merida1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘epimutacions/DESCRIPTION’ ... OK
* preparing ‘epimutacions’:
* 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 ‘epimutacions_0.99.18.tar.gz’
merida1 CHECK output
[top]
===============================
BiocCheckGitClone('epimutacions')
===============================
This is BiocCheckGitClone version 1.31.23. 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
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2294/1513920f2d2e68741ff26fac50f670df3743761b/epimutacions.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 ‘epimutacions/DESCRIPTION’ ... OK
* this is package ‘epimutacions’ version ‘0.99.18’
* 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 ‘epimutacions’ can be installed ... [42s/42s] OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [43s/43s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [24s/30s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
epimutations 3.566 0.513 10.523
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [27s/29s]
[27s/29s] 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: OK
===============================
BiocCheck('epimutacions_0.99.18.tar.gz')
===============================
This is BiocCheck version 1.31.23. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
* 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...
* 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 epimutacions...
* Checking coding practice...
* NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
R/mlm.R (line 94, column 16)
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2
times)
suppressWarnings() in R/epimutations.R (line 322, column 17)
suppressMessages() in R/epimutations.R (line 232, column 7)
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 14 functions > 50 lines.
The longest 5 functions are:
epimutations() (R/epimutations.R, line 109): 327 lines
plot_epimutations() (R/plot_epimutations.R, line 69): 233 lines
epi_quantile() (R/epi_quantile.R, line 41): 208 lines
mlmtst() (R/mlmtst.R, line 43): 139 lines
mlm() (R/mlm.R, line 82): 131 lines
* Checking man page documentation...
* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
epi_preprocess.Rd
* NOTE: Usage of dontrun{} / donttest{} found in man page examples.
8% of man pages use one of these cases.
Found in the following files:
annotate_epimutations.Rd
epimutations_one_leave_out.Rd
plot_epimutations.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; 127 lines (2%) are > 80 characters
long.
First 6 lines:
man/epi_parameters.Rd:13 quantile = list(window_sz = 1000, offset_abs...
man/norm_parameters.Rd:8 illumina = list(bg.correct = TRUE, normalize...
man/norm_parameters.Rd:9 quantile = list(fixOutliers = TRUE, removeBa...
man/norm_parameters.Rd:10 quantileNormalize = TRUE, stratified = TR...
man/norm_parameters.Rd:11 noob = list(offset = 15, dyeCorr = TRUE, dy...
man/norm_parameters.Rd:12 funnorm = list(nPCs = 2, sex = NULL, bgCorr...
* NOTE: Consider 4 spaces instead of tabs; 280 lines (5%) contain
tabs.
First 6 lines:
R/add_ensemble_regulatory.R:68 bm <- biomaRt::getBM(
R/add_ensemble_regulatory.R:69 attributes = c("activity",
R/add_ensemble_regulatory.R:70 "regulatory_stable_id",
R/add_ensemble_regulatory.R:71 "chromosome_name",
R/add_ensemble_regulatory.R:72 "chromosome_start",
R/add_ensemble_regulatory.R:73 "chromosome_end",
* NOTE: Consider multiples of 4 spaces for line indents, 1476
lines(25%) are not.
First 6 lines:
R/add_ensemble_regulatory.R:31 ## Remove chr from chromosome
R/add_ensemble_regulatory.R:32 epimutations$chromosome <- gsub("chr",
R/add_ensemble_regulatory.R:33 "",
R/add_ensemble_regulatory.R:34 epimut...
R/add_ensemble_regulatory.R:35 ## Create connection to ENSEMBL
R/add_ensemble_regulatory.R:36
See http://bioconductor.org/developers/how-to/coding-style/
See styler package: https://cran.r-project.org/package=styler as
described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 8
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
merida1 BUILD BIN output
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===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir epimutacions_0.99.18.tar.gz'
>>>>>>>
* installing *source* package ‘epimutacions’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c mlm_init.c -o mlm_init.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c ruben.cpp -o ruben.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -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 epimutacions.so mlm_init.o ruben.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/pkgbuild/packagebuilder/workers/jobs/2294/1513920f2d2e68741ff26fac50f670df3743761b/libdir/00LOCK-epimutacions/00new/epimutacions/libs
** R
** data
** 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 (epimutacions)
>>>>>>>
>>>>>>> FIXING LINKS FOR libdir/epimutacions/libs/epimutacions.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/epimutacions/libs/epimutacions.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgfortran.5.dylib" "libdir/epimutacions/libs/epimutacions.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libquadmath.0.dylib" "libdir/epimutacions/libs/epimutacions.so"
nebbiolo1 Summary
[top]
| Package: epimutacions |
| Version: 0.99.18 |
| RVersion: 4.2
|
| BiocVersion: 3.15
|
| BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data epimutacions |
| BuildTime: 3 minutes 44.13 seconds |
| CheckCommand: BiocCheckGitClone('epimutacions') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings epimutacions_0.99.18.tar.gz && BiocCheck('epimutacions_0.99.18.tar.gz', `new-package`=TRUE) |
| CheckTime: 4 minutes 33.39 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 1651.63 KiB |
| BuildID:: epimutacions_20220112162826 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: epimutacions. 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. Checking Package status: 0. |
nebbiolo1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘epimutacions/DESCRIPTION’ ... OK
* preparing ‘epimutacions’:
* 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 ‘epimutacions_0.99.18.tar.gz’
nebbiolo1 CHECK output
[top]
===============================
BiocCheckGitClone('epimutacions')
===============================
This is BiocCheckGitClone version 1.31.23. 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
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2294/1513920f2d2e68741ff26fac50f670df3743761b/epimutacions.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 ‘epimutacions/DESCRIPTION’ ... OK
* this is package ‘epimutacions’ version ‘0.99.18’
* 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 ‘epimutacions’ can be installed ... [29s/29s] OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [30s/30s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [19s/20s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [27s/23s]
[28s/23s] 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: OK
===============================
BiocCheck('epimutacions_0.99.18.tar.gz')
===============================
This is BiocCheck version 1.31.23. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
* 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...
* 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 epimutacions...
* Checking coding practice...
* NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
R/mlm.R (line 94, column 16)
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2
times)
suppressWarnings() in R/epimutations.R (line 322, column 17)
suppressMessages() in R/epimutations.R (line 232, column 7)
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 14 functions > 50 lines.
The longest 5 functions are:
epimutations() (R/epimutations.R, line 109): 327 lines
plot_epimutations() (R/plot_epimutations.R, line 69): 233 lines
epi_quantile() (R/epi_quantile.R, line 41): 208 lines
mlmtst() (R/mlmtst.R, line 43): 139 lines
mlm() (R/mlm.R, line 82): 131 lines
* Checking man page documentation...
* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
epi_preprocess.Rd
* NOTE: Usage of dontrun{} / donttest{} found in man page examples.
8% of man pages use one of these cases.
Found in the following files:
annotate_epimutations.Rd
epimutations_one_leave_out.Rd
plot_epimutations.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; 127 lines (2%) are > 80 characters
long.
First 6 lines:
man/epi_parameters.Rd:13 quantile = list(window_sz = 1000, offset_abs...
man/norm_parameters.Rd:8 illumina = list(bg.correct = TRUE, normalize...
man/norm_parameters.Rd:9 quantile = list(fixOutliers = TRUE, removeBa...
man/norm_parameters.Rd:10 quantileNormalize = TRUE, stratified = TR...
man/norm_parameters.Rd:11 noob = list(offset = 15, dyeCorr = TRUE, dy...
man/norm_parameters.Rd:12 funnorm = list(nPCs = 2, sex = NULL, bgCorr...
* NOTE: Consider 4 spaces instead of tabs; 280 lines (5%) contain
tabs.
First 6 lines:
R/add_ensemble_regulatory.R:68 bm <- biomaRt::getBM(
R/add_ensemble_regulatory.R:69 attributes = c("activity",
R/add_ensemble_regulatory.R:70 "regulatory_stable_id",
R/add_ensemble_regulatory.R:71 "chromosome_name",
R/add_ensemble_regulatory.R:72 "chromosome_start",
R/add_ensemble_regulatory.R:73 "chromosome_end",
* NOTE: Consider multiples of 4 spaces for line indents, 1476
lines(25%) are not.
First 6 lines:
R/add_ensemble_regulatory.R:31 ## Remove chr from chromosome
R/add_ensemble_regulatory.R:32 epimutations$chromosome <- gsub("chr",
R/add_ensemble_regulatory.R:33 "",
R/add_ensemble_regulatory.R:34 epimut...
R/add_ensemble_regulatory.R:35 ## Create connection to ENSEMBL
R/add_ensemble_regulatory.R:36
See http://bioconductor.org/developers/how-to/coding-style/
See styler package: https://cran.r-project.org/package=styler as
described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 8
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
nebbiolo1 BUILD BIN output
[top]