Bioconductor Single Package Builder - Build History

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

 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_0.99.16.tar.gz’

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

 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/af73a8b130d67698f9e024dcffb88198e35e5142/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 ‘0.99.16’
* 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 ... [77s/78s] 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 ... [81s/83s] 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 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/99s] ERROR
Running examples in ‘epimutacions-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: annotate_epimutations
> ### Title: Annotate the results of epimutations or
> ###   epimutations_one_leave_out functions
> ### Aliases: annotate_epimutations
> 
> ### ** Examples
> 
> 
> data(res.epi.manova)
> 
> #Annotate the epimutations
> 
> anno_results <- annotate_epimutations(res.epi.manova)
Loading DB
Loading required package: IlluminaHumanMethylationEPICanno.ilm10b2.hg19
Loading required package: minfi
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: ‘MatrixGenerics’

The following objects are masked from ‘package:matrixStats’:

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: ‘Biobase’

The following object is masked from ‘package:MatrixGenerics’:

    rowMedians

The following objects are masked from ‘package:matrixStats’:

    anyMissing, rowMedians

Loading required package: Biostrings
Loading required package: XVector

Attaching package: ‘Biostrings’

The following object is masked from ‘package:base’:

    strsplit

Loading required package: bumphunter
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
Loading required package: locfit
locfit 1.5-9.4 	 2020-03-24
Annotating:
GencodeBasicV12_NAME
Regulatory_Feature_Group
Relation_to_Island
- Extracting and annotating OMIMs
Warning: Ensembl will soon enforce the use of https.
Ensure the 'host' argument includes "https://"
Ensembl site unresponsive, trying uswest mirror
Ensembl site unresponsive, trying asia mirror
Error in textConnection(text, encoding = "UTF-8") : 
  invalid 'text' argument
Calls: annotate_epimutations ... .getFilters -> .getAttrFilt -> read.table -> textConnection
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [52s/53s]
 [52s/54s] 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 ERROR, 1 NOTE
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/2294/af73a8b130d67698f9e024dcffb88198e35e5142/epimutacions.Rcheck/00check.log’
for details.





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

 BiocCheck('epimutacions_0.99.16.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...
    * 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:
        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 67): 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
* 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; 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, 1454
      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: 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

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

 R CMD BUILD

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

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir epimutacions_0.99.16.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/af73a8b130d67698f9e024dcffb88198e35e5142/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"