Bioconductor Single Package Builder - Build History

Snapshot Date: 
URL:  https://git.bioconductor.org/packages/epimutacions
Last Changed Rev:  / Revision: 
Last Changed Date: 

Hostname OS /Arch BUILD CHECK BUILD BIN POST-PROCESSING
merida1 macOS 10.14.6 Mojave/x86_64   OK     ERROR     OK     OK  
nebbiolo1 Linux (Ubuntu 20.04.4 LTS)/x86_64   OK     OK     skipped     OK  

merida1 Summary

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Package: epimutacions
Version: 0.99.14
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: 5 minutes 52.92 seconds
CheckCommand: BiocCheckGitClone('epimutacions') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch epimutacions_0.99.14.tar.gz && BiocCheck('epimutacions_0.99.14.tar.gz', `new-package`=TRUE)
CheckTime: 8 minutes 36.13 seconds
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh epimutacions_0.99.14.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir
BuildBinTime: 0 minutes 55.01 seconds
PackageFileSize: 237245.83 KiB
BuildID:: epimutacions_20220105140608
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: 1. Build Package status: 0.

merida1 BUILD SRC output

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

 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_0.99.14.tar.gz’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘epimutacions/vignettes/epimutacions_cache/html/plot_mvo_genes_annot_d09051d75898544e883c0bbdf4dfd30b.RData’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘epimutacions/vignettes/epimutacions_cache/html/plot_mvo_genes_annot_d09051d75898544e883c0bbdf4dfd30b.rdb’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘epimutacions/vignettes/epimutacions_cache/html/plot_mvo_genes_annot_d09051d75898544e883c0bbdf4dfd30b.rdx’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘epimutacions/vignettes/epimutacions_cache/html/plot_mvo_regulation_5cdd48fed17a91b4e3569c397c80beba.RData’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘epimutacions/vignettes/epimutacions_cache/html/plot_mvo_regulation_5cdd48fed17a91b4e3569c397c80beba.rdb’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘epimutacions/vignettes/epimutacions_cache/html/plot_mvo_regulation_5cdd48fed17a91b4e3569c397c80beba.rdx’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘epimutacions/vignettes/epimutacions_cache/html/unnamed-chunk-10_89348743876b8eac420831f399144112.RData’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘epimutacions/vignettes/epimutacions_cache/html/unnamed-chunk-11_f65af79145054e049f6eba322311b7bb.RData’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘epimutacions/vignettes/epimutacions_cache/html/unnamed-chunk-12_2b7d690614f636ac1b6edecad518aa63.RData’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘epimutacions/vignettes/epimutacions_cache/html/unnamed-chunk-13_37a6af79e61e200c6b534c4572dec968.RData’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘epimutacions/vignettes/epimutacions_cache/html/unnamed-chunk-14_ca71ffb7297a04485e85ed2a1f756470.RData’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘epimutacions/vignettes/epimutacions_cache/html/unnamed-chunk-15_f8c752d9d124ec590cfc213534566037.RData’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘epimutacions/vignettes/epimutacions_cache/html/unnamed-chunk-16_9674ef2124d2812af1cfc0c131eea3f4.RData’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘epimutacions/vignettes/epimutacions_cache/html/unnamed-chunk-17_1571d7ec5a012d675375243bcaa72fd0.RData’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘epimutacions/vignettes/epimutacions_cache/html/unnamed-chunk-18_540ed50b03e35c8e137a24843f43fa9d.RData’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘epimutacions/vignettes/epimutacions_cache/html/unnamed-chunk-19_67be84c8606b9e4b51acb68f26813a83.RData’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘epimutacions/vignettes/epimutacions_cache/html/unnamed-chunk-1_abf9ca8ccc7928adab2d27c638f2e533.RData’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘epimutacions/vignettes/epimutacions_cache/html/unnamed-chunk-20_9c444800f402a2ec5f1017d1c4b5dcf7.RData’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘epimutacions/vignettes/epimutacions_cache/html/unnamed-chunk-2_aa8224877337fc41c8938073e602e64b.RData’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘epimutacions/vignettes/epimutacions_cache/html/unnamed-chunk-3_205a7ba258b98329df0bb33c551dc211.RData’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘epimutacions/vignettes/epimutacions_cache/html/unnamed-chunk-4_7860887b91aa875a830bb4940c8eb5ef.RData’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘epimutacions/vignettes/epimutacions_cache/html/unnamed-chunk-5_d3ca2d1a63693aa884807c926e06ac55.RData’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘epimutacions/vignettes/epimutacions_cache/html/unnamed-chunk-6_40e47570d13a5fb7e3519f4d5d00d4b5.RData’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘epimutacions/vignettes/epimutacions_cache/html/unnamed-chunk-7_ab87b01643e1df7e40eebe2b77d75992.RData’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘epimutacions/vignettes/epimutacions_cache/html/unnamed-chunk-8_e12b00974cfbc47545f7c7d78a03e2ac.RData’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘epimutacions/vignettes/epimutacions_cache/html/unnamed-chunk-9_80a2d9c28349a9d2178c0416143cdd77.RData’

merida1 CHECK output

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

 BiocCheckGitClone('epimutacions')

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

This is BiocCheckGitClone version 1.31.19. 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/2294/7d35b594eebcc0e5308200ba1ad20873f9d5966e/epimutacions.Rcheck’
* using R Under development (unstable) (2021-11-01 r81125)
* 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 ‘0.99.14’
* 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 ... WARNING
Found the following files with non-portable file names:
  vignettes/epimutacions_cache/html/IDAT files_f27a5dcc1ee86fbaa9df63d6011acfb0.RData
  vignettes/epimutacions_cache/html/IDAT files_f27a5dcc1ee86fbaa9df63d6011acfb0.rdb
  vignettes/epimutacions_cache/html/IDAT files_f27a5dcc1ee86fbaa9df63d6011acfb0.rdx
  vignettes/epimutacions_cache/html/ann results_89e9c4b540da3989362ead752f45b104.RData
  vignettes/epimutacions_cache/html/ann results_89e9c4b540da3989362ead752f45b104.rdb
  vignettes/epimutacions_cache/html/ann results_89e9c4b540da3989362ead752f45b104.rdx
These are not fully portable file names.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
Found the following non-portable file paths:
  epimutacions/vignettes/epimutacions_cache/html/plot_mvo_genes_annot_d09051d75898544e883c0bbdf4dfd30b.RData
  epimutacions/vignettes/epimutacions_cache/html/plot_mvo_genes_annot_d09051d75898544e883c0bbdf4dfd30b.rdb
  epimutacions/vignettes/epimutacions_cache/html/plot_mvo_genes_annot_d09051d75898544e883c0bbdf4dfd30b.rdx
  epimutacions/vignettes/epimutacions_cache/html/plot_mvo_regulation_5cdd48fed17a91b4e3569c397c80beba.RData
  epimutacions/vignettes/epimutacions_cache/html/plot_mvo_regulation_5cdd48fed17a91b4e3569c397c80beba.rdb
  epimutacions/vignettes/epimutacions_cache/html/plot_mvo_regulation_5cdd48fed17a91b4e3569c397c80beba.rdx
  epimutacions/vignettes/epimutacions_cache/html/unnamed-chunk-10_89348743876b8eac420831f399144112.RData
  epimutacions/vignettes/epimutacions_cache/html/unnamed-chunk-11_f65af79145054e049f6eba322311b7bb.RData
  epimutacions/vignettes/epimutacions_cache/html/unnamed-chunk-12_2b7d690614f636ac1b6edecad518aa63.RData
  epimutacions/vignettes/epimutacions_cache/html/unnamed-chunk-13_37a6af79e61e200c6b534c4572dec968.RData
  epimutacions/vignettes/epimutacions_cache/html/unnamed-chunk-14_ca71ffb7297a04485e85ed2a1f756470.RData
  epimutacions/vignettes/epimutacions_cache/html/unnamed-chunk-15_f8c752d9d124ec590cfc213534566037.RData
  epimutacions/vignettes/epimutacions_cache/html/unnamed-chunk-16_9674ef2124d2812af1cfc0c131eea3f4.RData
  epimutacions/vignettes/epimutacions_cache/html/unnamed-chunk-17_1571d7ec5a012d675375243bcaa72fd0.RData
  epimutacions/vignettes/epimutacions_cache/html/unnamed-chunk-18_540ed50b03e35c8e137a24843f43fa9d.RData
  epimutacions/vignettes/epimutacions_cache/html/unnamed-chunk-19_67be84c8606b9e4b51acb68f26813a83.RData
  epimutacions/vignettes/epimutacions_cache/html/unnamed-chunk-1_abf9ca8ccc7928adab2d27c638f2e533.RData
  epimutacions/vignettes/epimutacions_cache/html/unnamed-chunk-20_9c444800f402a2ec5f1017d1c4b5dcf7.RData
  epimutacions/vignettes/epimutacions_cache/html/unnamed-chunk-2_aa8224877337fc41c8938073e602e64b.RData
  epimutacions/vignettes/epimutacions_cache/html/unnamed-chunk-3_205a7ba258b98329df0bb33c551dc211.RData
  epimutacions/vignettes/epimutacions_cache/html/unnamed-chunk-4_7860887b91aa875a830bb4940c8eb5ef.RData
  epimutacions/vignettes/epimutacions_cache/html/unnamed-chunk-5_d3ca2d1a63693aa884807c926e06ac55.RData
  epimutacions/vignettes/epimutacions_cache/html/unnamed-chunk-6_40e47570d13a5fb7e3519f4d5d00d4b5.RData
  epimutacions/vignettes/epimutacions_cache/html/unnamed-chunk-7_ab87b01643e1df7e40eebe2b77d75992.RData
  epimutacions/vignettes/epimutacions_cache/html/unnamed-chunk-8_e12b00974cfbc47545f7c7d78a03e2ac.RData
  epimutacions/vignettes/epimutacions_cache/html/unnamed-chunk-9_80a2d9c28349a9d2178c0416143cdd77.RData

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘epimutacions’ can be installed ... [43s/43s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘testthat’
A package should be listed in only one of these fields.
* 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 ... [74s/140s] OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
annotate_epimutations      33.367  1.663  99.413
epimutations_one_leave_out  4.371  0.159   5.063
* 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: 1 WARNING, 1 NOTE
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/2294/7d35b594eebcc0e5308200ba1ad20873f9d5966e/epimutacions.Rcheck/00check.log’
for details.






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

 BiocCheck('epimutacions_0.99.14.tar.gz')

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

This is BiocCheck version 1.31.19. 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...
    * NOTE: Update R version dependency from 4.1.0 to 4.2.0.
* Checking package size...
    * ERROR: Package Source tarball exceeds Bioconductor size
      requirement.
        Package Size: 242.9397 MB
        Size Requirement: 5.0000 MB
* Checking individual file sizes...
    * WARNING: The following files are over 5MB in size:
      'vignettes/epimutacions_cache/html/FALSE_23ca699869d450beccb86e26688b65a1.rdb
      vignettes/epimutacions_cache/html/unnamed-chunk-12_2b7d690614f636ac1b6edecad518aa63.rdb'
* 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:
        = in 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 73): 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...
* 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; 173 lines (3%) 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; 275 lines (5%) contain
      tabs.
    First 6 lines:
      R/add_ensemble_regulatory.R:61 	bm <- biomaRt::getBM(attributes = c("ac...
      R/add_ensemble_regulatory.R:62 	                                    "re...
      R/add_ensemble_regulatory.R:63 	                                    "ch...
      R/add_ensemble_regulatory.R:64 	                                    "ch...
      R/add_ensemble_regulatory.R:65 	                                    "ch...
      R/add_ensemble_regulatory.R:66 	                                    "fe...
    * NOTE: Consider multiples of 4 spaces for line indents, 1436
      lines(25%) are not.
    First 6 lines:
      R/add_ensemble_regulatory.R:30   ## Remove chr from chromosome
      R/add_ensemble_regulatory.R:31   epimutations$chromosome <- gsub("chr",...
      R/add_ensemble_regulatory.R:32   ## Create connection to ENSEMBL 
      R/add_ensemble_regulatory.R:33   
      R/add_ensemble_regulatory.R:34   mart <- biomaRt::useEnsembl(biomart = ...
      R/add_ensemble_regulatory.R:35   ensembl <- biomaRt::useDataset(dataset...
    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: 1
WARNING count: 1
NOTE count: 7
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

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

 R CMD BUILD

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

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir epimutacions_0.99.14.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/2294/7d35b594eebcc0e5308200ba1ad20873f9d5966e/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

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Package: epimutacions
Version: 0.99.14
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: 4 minutes 43.66 seconds
CheckCommand: BiocCheckGitClone('epimutacions') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings epimutacions_0.99.14.tar.gz && BiocCheck('epimutacions_0.99.14.tar.gz', `new-package`=TRUE)
CheckTime: 5 minutes 54.92 seconds
BuildBinCommand:
BuildBinTime:
PackageFileSize: 1650.21 KiB
BuildID:: epimutacions_20220105140608
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

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

 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_0.99.14.tar.gz’

nebbiolo1 CHECK output

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

 BiocCheckGitClone('epimutacions')

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

This is BiocCheckGitClone version 1.31.19. 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/2294/7d35b594eebcc0e5308200ba1ad20873f9d5966e/epimutacions.Rcheck’
* using R Under development (unstable) (2021-11-10 r81171)
* 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 ‘0.99.14’
* 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 ... [31s/31s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘testthat’
A package should be listed in only one of these fields.
* 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 ... [31s/31s] 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 ... [59s/96s] OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
annotate_epimutations 24.463  2.088  61.581
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [41s/22s]
 [41s/22s] 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: 1 NOTE
See
  ‘/home/pkgbuild/packagebuilder/workers/jobs/2294/7d35b594eebcc0e5308200ba1ad20873f9d5966e/epimutacions.Rcheck/00check.log’
for details.






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

 BiocCheck('epimutacions_0.99.14.tar.gz')

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

This is BiocCheck version 1.31.19. 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...
    * NOTE: Update R version dependency from 4.1.0 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 epimutacions...
* Checking coding practice...
    * NOTE: Avoid using '=' for assignment and use '<-' instead
      Found in files:
        = in 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 73): 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...
* 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; 173 lines (3%) 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; 275 lines (5%) contain
      tabs.
    First 6 lines:
      R/add_ensemble_regulatory.R:61 	bm <- biomaRt::getBM(attributes = c("ac...
      R/add_ensemble_regulatory.R:62 	                                    "re...
      R/add_ensemble_regulatory.R:63 	                                    "ch...
      R/add_ensemble_regulatory.R:64 	                                    "ch...
      R/add_ensemble_regulatory.R:65 	                                    "ch...
      R/add_ensemble_regulatory.R:66 	                                    "fe...
    * NOTE: Consider multiples of 4 spaces for line indents, 1436
      lines(25%) are not.
    First 6 lines:
      R/add_ensemble_regulatory.R:30   ## Remove chr from chromosome
      R/add_ensemble_regulatory.R:31   epimutations$chromosome <- gsub("chr",...
      R/add_ensemble_regulatory.R:32   ## Create connection to ENSEMBL 
      R/add_ensemble_regulatory.R:33   
      R/add_ensemble_regulatory.R:34   mart <- biomaRt::useEnsembl(biomart = ...
      R/add_ensemble_regulatory.R:35   ensembl <- biomaRt::useDataset(dataset...
    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: 7
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

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