Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘seqpac/DESCRIPTION’ ... OK
* preparing ‘seqpac’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
Omitted ‘LazyData’ from DESCRIPTION
* building ‘seqpac_0.99.1.tar.gz’

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 BiocCheckGitClone('seqpac')

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This is BiocCheckGitClone version 1.31.15. 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:
        seqpac.Rproj
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
    * NOTE: CITATION file might be not correctly formatted


Summary:
ERROR count: 1
WARNING count: 0
NOTE count: 1
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.




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 R CMD CHECK

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* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2275/seqpac_20211213074351/seqpac.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 ‘seqpac/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘seqpac’ version ‘0.99.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘seqpac’ can be installed ... [14s/14s] OK
* checking installed package size ... NOTE
  installed size is 29.9Mb
  sub-directories of 1Mb or more:
    extdata  28.4Mb
* 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 ... [21s/21s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [58s/58s] ERROR
Running examples in ‘seqpac-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PAC_gtf
> ### Title: Annotate against a GTF file
> ### Aliases: PAC_gtf
> 
> ### ** Examples
> 
> 
> # Load PAC
> load(system.file("extdata", "drosophila_sRNA_pac_filt_anno.Rdata", 
+                  package = "seqpac", mustWork = TRUE))
> 
> # Create a gtf file from PAC coordinates
> anno <- pac$Anno
> anno <- anno[!grepl("Warning", anno$mis0_chromosomes_genome),]
> anno <- anno[!is.na(anno$mis0_chromosomes_genome),]
> coord <- anno$mis0_chromosomes_genome
> coord <- suppressWarnings(do.call("rbind", strsplit(coord, "\\|"))[,1])
> coord <- suppressWarnings(do.call("rbind", strsplit(coord, "\\;start=|;")))
> gr <- GenomicRanges::GRanges(seqnames=coord[,1], 
+                              IRanges::IRanges(as.numeric(coord[,2]), 
+                                               as.numeric(coord[,2])+anno$Size ), 
+                              strand=coord[,3])
> 
> GenomicRanges::mcols(gr) <- data.frame(biotype=anno$Biotypes_mis3, 
+                                        bio_zero=as.character(anno$mis0_bio))
> spl <- sample(1:length(gr), round(length(gr)*0.3), replace=FALSE)
> gr1 <- gr[spl]
> gr2 <- gr[!1:length(gr) %in% spl]
> 
> # Prepare temp folder and save artifical gtf
> out1 <- paste0(tempdir(), "/temp1.gtf")
> out2 <- paste0(tempdir(), "/temp2.gtf")
> 
> rtracklayer::export(gr1, out1, format="gtf")
> rtracklayer::export(gr2, out2, format="gtf")
> 
> # Make sure PAC contains full genome coordinates
> # (In the add_reanno function you may choose how many coordinates to report)
> # (If there are more, a 'Warning' will be added to the annotation)
> # (Here we remove those to avoid problems)
> 
> new_anno <-  pac$Anno [, grepl("chromosomes_genome|Size", colnames(pac$Anno))]
> test <- new_anno[, 3:ncol(new_anno)]
> test <- apply(test, 2, function(x){substr(x, 1, 7)})
> test <- apply(test, 1, function(x){paste(x, collapse = "")})
> new_anno$temp <- ifelse(grepl("Warning",  test), "rm", "keep")
> pac$Anno <- new_anno
> pac <- PAC_filter(pac, subset_only=TRUE, anno_target=list("temp", "keep"))	

-- Anno target was specified, will retain: 7442 of 9131 seqs.> 
> #  Run PAC_gtf
> gtf <- list(gtf1=out1, gtf2=out2)
> target <- list(gtf1=c("biotype","bio_zero"), gtf2=c("biotype","bio_zero"))
> 
> pac_merge <- PAC_gtf(pac, mismatches=0, return="merge", 
+                     gtf=gtf, target=target, threads=8)

Importing gtf files ...

Reorganizing coordinates ...

Chromosome names compatibility check ...
  -- Note, not all chrosomsome names were represented in 'gtf_gtf1'.
     Could be wise to double check that chrosomsome names 
     are compatible.

Annotating against the gtf file(s)  ...Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

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

    colnames, counts, counts<-, rownames

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: S4Vectors

Attaching package: ‘S4Vectors’

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Error in .check_ncores(cores) : 8 simultaneous processes spawned
Calls: PAC_gtf ... %dopar% -> <Anonymous> -> mclapply -> .check_ncores
Execution halted
* 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/2275/seqpac_20211213074351/seqpac.Rcheck/00check.log’
for details.





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 BiocCheck('seqpac_0.99.1.tar.gz')

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This is BiocCheck version 1.31.15. 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...
    Workflow
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
    * NOTE: Consider adding these automatically suggested biocViews:
      BasicWorkflow
See http://bioconductor.org/developers/how-to/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...
    * NOTE: License 'file LICENSE' unknown; licenses cannot restrict
      use
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
    * NOTE: Potential intermediate files found:
        vignettes/seqpac_-_a_guide_to_srna_analysis_using_sequence-based_counts.html
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of seqpac...
* Checking coding practice...
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
      Found in files:
        add_reanno.R (line 246, column 15)
        add_reanno.R (line 251, column 17)
        add_reanno.R (line 301, column 16)
        add_reanno.R (line 318, column 15)
        add_reanno.R (line 324, column 17)
        add_reanno.R (line 445, column 49)
        add_reanno.R (line 449, column 55)
        filtsep_bin.R (line 70, column 15)
        import_reanno.R (line 107, column 13)
        import_reanno.R (line 171, column 51)
        make_conv.R (line 154, column 12)
        make_conv.R (line 189, column 14)
        make_conv.R (line 226, column 12)
        make_conv.R (line 290, column 14)
        make_conv.R (line 292, column 40)
        make_counts.R (line 401, column 35)
        make_counts.R (line 487, column 35)
        make_counts.R (line 552, column 40)
        make_cutadapt.R (line 178, column 37)
        make_pheno.R (line 207, column 16)
        make_pheno.R (line 214, column 16)
        make_reanno.R (line 209, column 16)
        make_reanno.R (line 211, column 12)
        make_reanno.R (line 263, column 14)
        make_reanno.R (line 268, column 18)
        make_reanno.R (line 295, column 15)
        make_trim.R (line 248, column 42)
        make_trim.R (line 305, column 7)
        make_trim.R (line 414, column 18)
        make_trim.R (line 623, column 53)
        make_trim.R (line 653, column 14)
        make_trim.R (line 666, column 12)
        map_rangetype.R (line 193, column 48)
        map_rangetype.R (line 216, column 14)
        map_rangetype.R (line 289, column 17)
        map_rangetype.R (line 376, column 14)
        map_rangetype.R (line 441, column 17)
        map_rangetype.R (line 447, column 17)
        map_reanno.R (line 342, column 12)
        map_reanno.R (line 349, column 15)
        merge_lanes.R (line 142, column 30)
        merge_lanes.R (line 149, column 14)
        PAC_check.R (line 116, column 52)
        PAC_check.R (line 125, column 54)
        PAC_covplot.R (line 232, column 14)
        PAC_covplot.R (line 251, column 14)
        PAC_covplot.R (line 275, column 12)
        PAC_covplot.R (line 281, column 36)
        PAC_covplot.R (line 285, column 30)
        PAC_covplot.R (line 293, column 54)
        PAC_covplot.R (line 314, column 12)
        PAC_deseq.R (line 133, column 13)
        PAC_filter.R (line 252, column 17)
        PAC_gtf.R (line 265, column 21)
        PAC_gtf.R (line 283, column 13)
        PAC_gtf.R (line 402, column 12)
        PAC_gtf.R (line 427, column 12)
        PAC_gtf.R (line 478, column 36)
        PAC_gtf.R (line 509, column 12)
        PAC_gtf.R (line 515, column 39)
        PAC_gtf.R (line 557, column 14)
        PAC_gtf.R (line 561, column 16)
        PAC_gtf.R (line 573, column 14)
        PAC_gtf.R (line 577, column 16)
        PAC_jitter.R (line 167, column 22)
        PAC_mapper.R (line 309, column 12)
        PAC_mapper.R (line 369, column 12)
        PAC_mapper.R (line 407, column 49)
        PAC_nbias.R (line 184, column 12)
        PAC_norm.R (line 61, column 15)
        PAC_pca.R (line 124, column 47)
        PAC_pie.R (line 166, column 15)
        PAC_pie.R (line 180, column 13)
        PAC_pie.R (line 192, column 24)
        PAC_pie.R (line 192, column 40)
        PAC_saturation.R (line 81, column 41)
        PAC_saturation.R (line 95, column 14)
        PAC_saturation.R (line 159, column 35)
        PAC_sizedist.R (line 173, column 14)
        PAC_sizedist.R (line 196, column 12)
        PAC_stackbar.R (line 152, column 15)
        PAC_stackbar.R (line 166, column 13)
        PAC_summary.R (line 144, column 50)
        PAC_trna.R (line 312, column 23)
        PAC_trna.R (line 332, column 16)
        simplify_reanno.R (line 301, column 23)
        simplify_reanno.R (line 363, column 15)
        simplify_reanno.R (line 381, column 12)
    * NOTE: Avoid the use of 'paste' in condition signals
      Found in files:
        R/make_cutadapt.R (line 165, column 10)
        R/make_reanno.R (line 321, column 12)
        R/make_reanno.R (line 343, column 15)
        R/make_trim.R (line 278, column 10)
        R/map_reanno.R (line 293, column 15)
        R/map_reanno.R (line 299, column 17)
        R/map_reanno.R (line 305, column 14)
        R/PAC_check.R (line 58, column 10)
        R/PAC_check.R (line 62, column 10)
        R/PAC_check.R (line 98, column 16)
        R/PAC_check.R (line 104, column 16)
        R/PAC_check.R (line 120, column 22)
        R/PAC_check.R (line 129, column 24)
        R/PAC_check.R (line 148, column 17)
        R/PAC_check.R (line 168, column 11)
        R/PAC_check.R (line 183, column 17)
        R/PAC_check.R (line 192, column 20)
        R/PAC_gtf.R (line 345, column 15)
        R/PAC_summary.R (line 107, column 12)
    * NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
      Found in files:
        R/PAC_filter.R (line 114, column 11)
        R/PAC_filter.R (line 227, column 12)
        R/PAC_filter.R (line 230, column 12)
        R/PAC_gtf.R (line 389, column 5)
* Checking parsed R code in R directory, examples, vignettes...
    Found @ in man/add_reanno.Rd
    Found @ in man/as.PAC.Rd
    Found @ in man/as.reanno.Rd
    Found @ in man/make_reanno.Rd
    Found @ in man/map_reanno.Rd
    Found @ in man/PAC.Rd
    Found @ in man/reanno.Rd
    Found @ in
      vignettes/seqpac_-_A_guide_to_sRNA_analysis_using_sequence-based_counts.Rmd
    * NOTE: Use accessors; don't access S4 class slots via '@' in
      examples/vignettes.
    * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 13
      times)
        suppressWarnings() in R/make_conv.R (line 293, column 7)
        suppressWarnings() in R/make_counts.R (line 253, column 7)
        suppressWarnings() in R/make_cutadapt.R (line 153, column 5)
        suppressWarnings() in R/make_trim.R (line 285, column 5)
        suppressWarnings() in R/map_reanno.R (line 309, column 5)
        suppressWarnings() in R/PAC_filter.R (line 259, column 7)
        suppressWarnings() in R/PAC_gtf.R (line 370, column 13)
        suppressWarnings() in R/PAC_gtf.R (line 527, column 17)
        suppressWarnings() in R/PAC_mapper.R (line 253, column 3)
        suppressWarnings() in R/PAC_mapper.R (line 257, column 3)
        suppressMessages() in R/PAC_pca.R (line 105, column 12)
        suppressMessages() in R/PAC_pca.R (line 109, column 12)
        suppressWarnings() in R/PAC_trna.R (line 466, column 9)
* Checking function lengths    * NOTE: Recommended function length <= 50 lines.
      There are 31 functions > 50 lines.
      The longest 5 functions are:
        make_trim() (R/make_trim.R, line 212): 526 lines
        make_counts() (R/make_counts.R, line 221): 401 lines
        PAC_gtf() (R/PAC_gtf.R, line 248): 369 lines
        PAC_trna() (R/PAC_trna.R, line 188): 366 lines
        add_reanno() (R/add_reanno.R, line 216): 278 lines
* Checking man page documentation...
    * NOTE: Consider adding runnable examples to the following man
      pages which document exported objects:
      import_reanno.Rd, map_rangetype.Rd, PAC_deseq.Rd, PAC_trna.Rd,
  tRNA_class.Rd
    * NOTE: Usage of dontrun{} / donttest{} found in man page examples.
      18% of man pages use one of these cases.
      Found in the following files:
        import_reanno.Rd
        make_conv.Rd
        make_cutadapt.Rd
        map_rangetype.Rd
        PAC_deseq.Rd
        PAC_gtf.Rd
        PAC_trna.Rd
        simplify_reanno.Rd
        tRNA_class.Rd
    * NOTE: Use donttest{} instead of dontrun{}.
      Found in the following files:
        import_reanno.Rd
        make_conv.Rd
        make_cutadapt.Rd
        map_rangetype.Rd
        PAC_deseq.Rd
        PAC_gtf.Rd
        PAC_trna.Rd
        simplify_reanno.Rd
        tRNA_class.Rd
* Checking package NEWS...
* Checking unit tests...
    * NOTE: Consider adding unit tests. We strongly encourage them. See
      http://bioconductor.org/developers/how-to/unitTesting-guidelines/.
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
  and vignette source...
    * NOTE: Consider shorter lines; 330 lines (2%) are > 80 characters
      long.
    First 6 lines:
      R/add_reanno.R:93 #' # Here we use the R temporary folder depending on ...
      R/add_reanno.R:103 #' ##  Then map your PAC-object against the fasta re...
      R/add_reanno.R:108 #' ##  Then import and generate a reanno-object of t...
      R/add_reanno.R:109 #' reanno_biotype <- make_reanno(output, PAC=pac, mi...
      R/filtsep_bin.R:39 #'  pac_filt <- PAC_filter(pac, subset_only = TRUE, ...
      R/filtsep_bin.R:66      df <- as.data.frame(matrix(NA, nrow=length(seqs...
    * NOTE: Consider 4 spaces instead of tabs; 5 lines (0%) contain
      tabs.
    First 5 lines:
      R/PAC_covplot.R:369         plot_lst[[i]] <- 	ggplot2::ggplot(cov_df, g...
      R/PAC_filter.R:267           ggplot2::ggtitle("User filter:")+					
      R/PAC_filter.R:285       ### Promt for user input					
      R/PAC_gtf.R:110 #' pac <- PAC_filter(pac, subset_only=TRUE, anno_target...
      man/PAC_gtf.Rd:124 pac <- PAC_filter(pac, subset_only=TRUE, anno_target...
    * NOTE: Consider multiples of 4 spaces for line indents, 4835
      lines(24%) are not.
    First 6 lines:
      R/add_reanno.R:217                        bio_perfect=FALSE, genome_max...
      R/add_reanno.R:218   
      R/add_reanno.R:219   if(isS4(reanno)){
      R/add_reanno.R:222   }else{
      R/add_reanno.R:224   }
      R/add_reanno.R:225   
    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: 0
NOTE count: 16
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.

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

 R CMD BUILD

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

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir seqpac_0.99.1.tar.gz'
>>>>>>> 

* installing *source* package ‘seqpac’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘norm’ in package ‘seqpac’
Creating a new generic function for ‘summary’ in package ‘seqpac’
Creating a generic function for ‘rownames’ from package ‘base’ in package ‘seqpac’
Creating a generic function for ‘colnames’ from package ‘base’ in package ‘seqpac’
Creating a generic function for ‘ncol’ from package ‘base’ in package ‘seqpac’
Creating a generic function for ‘nrow’ from package ‘base’ in package ‘seqpac’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (seqpac)