Bioconductor Single Package Builder - Build History

Snapshot Date:

URL: https://git.bioconductor.org/packages/seqpac

Last Changed Rev: / Revision:

Last Changed Date:

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

nebbiolo1 Summary

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Package: seqpac

Version: 0.99.5

RVersion: 4.2

BiocVersion: 3.15

BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data seqpac

BuildTime: 1 minutes 31.51 seconds

CheckCommand: BiocCheckGitClone('seqpac') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings seqpac_0.99.5.tar.gz && BiocCheck('seqpac_0.99.5.tar.gz', `new-package`=TRUE)

CheckTime: 10 minutes 19.00 seconds

BuildBinCommand:

BuildBinTime:

PackageFileSize: 3761.52 KiB

BuildID:: seqpac_20220203141155

PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: seqpac. Starting Build package. Starting Check package.

PostProcessing: Finished Git clone. Package type: Workflow. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 1.

nebbiolo1 BUILD SRC output

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

 R CMD BUILD

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

* 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_0.99.5.tar.gz’

nebbiolo1 CHECK output

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

 BiocCheckGitClone('seqpac')

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

This is BiocCheckGitClone version 1.31.31. 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...
* Checking that provided CITATION file is correctly formatted...


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/2275/e11a97c319d683aaa2b181e34c4e4b77d31754a8/seqpac.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 ‘seqpac/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘seqpac’ version ‘0.99.5’
* 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 ‘seqpac’ can be installed ... [7s/7s] OK
* checking installed package size ... NOTE
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       1.4Mb
    extdata   3.0Mb
* 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 ... [10s/10s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [421s/347s] OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
make_counts     41.954  5.527  34.437
PAC_deseq       26.686  7.743  22.391
map_reanno      23.877  6.003  22.931
make_PAC        22.626  2.577  18.850
make_pheno      21.448  2.426  17.278
PAC_gtf         20.212  2.587  13.551
make_trim       19.470  0.344  19.814
make_cutadapt   19.145  0.248  19.394
PAC_covplot     15.771  0.488  16.259
PAC_mapper      14.195  0.486  14.684
add_reanno      11.080  2.807  12.512
tRNA_class       5.582  5.322   7.587
PAC_trna         5.468  5.101   7.347
reanno           8.352  2.188   9.237
simplify_reanno  8.189  2.067   8.948
overview         7.337  2.082   8.130
names            7.132  2.268   8.114
as.reanno        7.110  1.783   7.649
full             6.362  1.859   6.991
map_rangetype    2.548  4.981   4.273
PAC_pca          5.790  0.056   5.846
make_reanno      4.317  1.321   4.843
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [395s/221s]
 [395s/221s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
          ])))
      df[1, ] <- gsub("  ", " ", as.character(unlist(df[1, ])))
      if (!is.null(parse[[1]])) {
          file.remove(temp_out)
      }
      return(df)
  }`: task 1 failed - "error in running command"
  Backtrace:
      ▆
   1. ├─seqpac quiet(...) at test_PAC_generation.R:64:4
   2. │ └─base::force(x) at test_PAC_generation.R:12:4
   3. └─seqpac::make_counts(...)
   4.   └─seqpac::make_cutadapt(...)
   5.     └─... %dopar% ...
   6.       └─e$fun(obj, substitute(ex), parent.frame(), e$data)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 31 ]
  Error: Test failures
  In addition: Warning message:
  In .Internal(gc(verbose, reset, full)) :
    closing unused connection 3 (/home/pkgbuild/packagebuilder/workers/jobs/2275/e11a97c319d683aaa2b181e34c4e4b77d31754a8/seqpac.Rcheck/seqpac/extdata/Stage3_Batch1_Inx13_S13.fastq.gz)
  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
  ‘/home/pkgbuild/packagebuilder/workers/jobs/2275/e11a97c319d683aaa2b181e34c4e4b77d31754a8/seqpac.Rcheck/00check.log’
for details.





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

 BiocCheck('seqpac_0.99.5.tar.gz')

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

This is BiocCheck version 1.31.31. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
Warning in system2(cmd, args, stdout = TRUE, stderr = FALSE, env = "R_DEFAULT_PACKAGES=NULL") :
  running command 'R_DEFAULT_PACKAGES=NULL '/home/biocbuild/bbs-3.15-bioc/R/bin/R' -q --vanilla --slave -f /home/biocbuild/bbs-3.15-bioc/R/library/BiocCheck/script/checkBadDeps.R --args "/home/pkgbuild/packagebuilder/workers/jobs/2275/e11a97c319d683aaa2b181e34c4e4b77d31754a8/seqpac_0.99.5.tar.gz" "/tmp/RtmpRa6wVf/file12ae838a424f1/lib" 2>/dev/null' had status 1
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R Version dependency...
    * NOTE: Update R version dependency from 4.1.0 to 4.2.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
    Workflow
* 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 seqpac...
* Checking coding practice...
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
      Found in files:
        add_reanno.R (line 264, column 15)
        add_reanno.R (line 269, column 17)
        add_reanno.R (line 319, column 16)
        add_reanno.R (line 343, column 17)
        add_reanno.R (line 464, column 49)
        add_reanno.R (line 468, column 55)
        filtsep_bin.R (line 68, column 12)
        import_reanno.R (line 137, column 13)
        import_reanno.R (line 201, column 51)
        make_conv.R (line 157, column 12)
        make_conv.R (line 192, column 14)
        make_conv.R (line 229, column 12)
        make_conv.R (line 291, column 14)
        make_counts.R (line 357, column 35)
        make_counts.R (line 443, column 35)
        make_counts.R (line 510, column 40)
        make_cutadapt.R (line 172, column 37)
        make_pheno.R (line 199, column 16)
        make_pheno.R (line 206, column 16)
        make_reanno.R (line 168, column 16)
        make_reanno.R (line 170, column 12)
        make_reanno.R (line 221, column 14)
        make_reanno.R (line 226, column 18)
        make_reanno.R (line 253, column 15)
        make_trim.R (line 242, column 42)
        make_trim.R (line 300, column 7)
        make_trim.R (line 409, column 18)
        make_trim.R (line 619, column 53)
        make_trim.R (line 649, column 14)
        make_trim.R (line 662, column 12)
        map_rangetype.R (line 129, column 48)
        map_rangetype.R (line 152, column 14)
        map_rangetype.R (line 225, column 17)
        map_rangetype.R (line 312, column 14)
        map_rangetype.R (line 377, column 17)
        map_rangetype.R (line 383, column 17)
        map_reanno.R (line 361, column 12)
        map_reanno.R (line 371, column 15)
        merge_lanes.R (line 142, column 30)
        merge_lanes.R (line 150, column 14)
        PAC_check.R (line 118, column 52)
        PAC_check.R (line 127, column 54)
        PAC_covplot.R (line 219, column 14)
        PAC_covplot.R (line 238, column 14)
        PAC_covplot.R (line 262, column 12)
        PAC_covplot.R (line 268, column 36)
        PAC_covplot.R (line 272, column 30)
        PAC_covplot.R (line 280, column 54)
        PAC_covplot.R (line 301, column 12)
        PAC_deseq.R (line 125, column 13)
        PAC_filter.R (line 253, column 17)
        PAC_gtf.R (line 143, column 21)
        PAC_gtf.R (line 161, column 13)
        PAC_gtf.R (line 280, column 12)
        PAC_gtf.R (line 305, column 12)
        PAC_gtf.R (line 356, column 36)
        PAC_gtf.R (line 387, column 12)
        PAC_gtf.R (line 393, column 39)
        PAC_gtf.R (line 438, column 14)
        PAC_gtf.R (line 442, column 16)
        PAC_gtf.R (line 454, column 14)
        PAC_gtf.R (line 458, column 16)
        PAC_jitter.R (line 167, column 22)
        PAC_mapper.R (line 260, column 12)
        PAC_mapper.R (line 320, column 12)
        PAC_mapper.R (line 358, column 49)
        PAC_nbias.R (line 186, column 12)
        PAC_norm.R (line 61, column 15)
        PAC_pca.R (line 129, column 47)
        PAC_pie.R (line 167, column 15)
        PAC_pie.R (line 181, column 13)
        PAC_pie.R (line 193, column 24)
        PAC_pie.R (line 193, column 40)
        PAC_saturation.R (line 86, column 41)
        PAC_saturation.R (line 102, column 14)
        PAC_saturation.R (line 188, column 35)
        PAC_sizedist.R (line 174, column 14)
        PAC_sizedist.R (line 197, column 12)
        PAC_stackbar.R (line 153, column 15)
        PAC_stackbar.R (line 167, column 13)
        PAC_summary.R (line 144, column 50)
        PAC_trna.R (line 339, column 23)
        PAC_trna.R (line 359, column 16)
        simplify_reanno.R (line 202, column 23)
        simplify_reanno.R (line 264, column 15)
        simplify_reanno.R (line 282, column 12)
    * NOTE: Avoid 'cat' and 'print' outside of 'show' methods
      Found in files:
        cat() in R/add_reanno.R (line 250, column 3)
        cat() in R/add_reanno.R (line 253, column 5)
        cat() in R/add_reanno.R (line 261, column 5)
        cat() in R/add_reanno.R (line 281, column 9)
        cat() in R/add_reanno.R (line 313, column 5)
        cat() in R/add_reanno.R (line 333, column 5)
        cat() in R/add_reanno.R (line 386, column 13)
        cat() in R/add_reanno.R (line 425, column 9)
        cat() in R/add_reanno.R (line 436, column 5)
        cat() in R/add_reanno.R (line 485, column 5)
        cat() in R/import_reanno.R (line 130, column 3)
        cat() in R/import_reanno.R (line 138, column 5)
        cat() in R/import_reanno.R (line 178, column 9)
        cat() in R/import_reanno.R (line 186, column 9)
        cat() in R/import_reanno.R (line 245, column 5)
        cat() in R/make_conv.R (line 121, column 3)
        cat() in R/make_conv.R (line 132, column 3)
        cat() in R/make_conv.R (line 143, column 7)
        cat() in R/make_conv.R (line 155, column 3)
        cat() in R/make_conv.R (line 190, column 5)
        cat() in R/make_conv.R (line 225, column 3)
        cat() in R/make_conv.R (line 305, column 3)
        cat() in R/make_counts.R (line 183, column 3)
        cat() in R/make_counts.R (line 196, column 5)
        cat() in R/make_counts.R (line 198, column 5)
        cat() in R/make_counts.R (line 200, column 3)
        cat() in R/make_counts.R (line 219, column 5)
        cat() in R/make_counts.R (line 220, column 5)
        cat() in R/make_counts.R (line 221, column 5)
        cat() in R/make_counts.R (line 222, column 5)
        cat() in R/make_counts.R (line 239, column 7)
        cat() in R/make_counts.R (line 240, column 7)
        cat() in R/make_counts.R (line 241, column 7)
        cat() in R/make_counts.R (line 243, column 7)
        cat() in R/make_counts.R (line 244, column 7)
        cat() in R/make_counts.R (line 246, column 7)
        cat() in R/make_counts.R (line 268, column 5)
        cat() in R/make_counts.R (line 269, column 5)
        cat() in R/make_counts.R (line 270, column 5)
        cat() in R/make_counts.R (line 271, column 5)
        cat() in R/make_counts.R (line 290, column 7)
        cat() in R/make_counts.R (line 291, column 7)
        cat() in R/make_counts.R (line 292, column 7)
        cat() in R/make_counts.R (line 293, column 7)
        cat() in R/make_counts.R (line 295, column 7)
        cat() in R/make_counts.R (line 296, column 7)
        cat() in R/make_counts.R (line 298, column 7)
        cat() in R/make_counts.R (line 299, column 7)
        cat() in R/make_counts.R (line 301, column 7)
        cat() in R/make_counts.R (line 302, column 7)
        cat() in R/make_counts.R (line 304, column 7)
        cat() in R/make_counts.R (line 341, column 3)
        cat() in R/make_counts.R (line 378, column 3)
        cat() in R/make_counts.R (line 410, column 5)
        cat() in R/make_counts.R (line 427, column 5)
        cat() in R/make_counts.R (line 431, column 7)
        cat() in R/make_counts.R (line 433, column 7)
        cat() in R/make_counts.R (line 470, column 3)
        print() in R/make_counts.R (line 201, column 3)
        print() in R/make_counts.R (line 242, column 7)
        print() in R/make_counts.R (line 245, column 7)
        print() in R/make_counts.R (line 294, column 7)
        print() in R/make_counts.R (line 297, column 7)
        print() in R/make_counts.R (line 300, column 7)
        print() in R/make_counts.R (line 303, column 7)
        print() in R/make_counts.R (line 568, column 5)
        cat() in R/make_cutadapt.R (line 135, column 3)
        cat() in R/make_cutadapt.R (line 136, column 3)
        cat() in R/make_pheno.R (line 221, column 5)
        cat() in R/make_pheno.R (line 226, column 7)
        cat() in R/make_pheno.R (line 228, column 5)
        cat() in R/make_pheno.R (line 236, column 5)
        cat() in R/make_pheno.R (line 256, column 5)
        cat() in R/make_pheno.R (line 261, column 3)
        print() in R/make_pheno.R (line 229, column 5)
        cat() in R/make_reanno.R (line 181, column 3)
        cat() in R/make_reanno.R (line 239, column 3)
        cat() in R/make_reanno.R (line 272, column 5)
        cat() in R/make_reanno.R (line 292, column 7)
        cat() in R/make_reanno.R (line 296, column 7)
        cat() in R/make_reanno.R (line 298, column 7)
        cat() in R/make_reanno.R (line 306, column 7)
        cat() in R/make_trim.R (line 225, column 5)
        cat() in R/make_trim.R (line 230, column 7)
        cat() in R/make_trim.R (line 234, column 5)
        cat() in R/make_trim.R (line 244, column 5)
        cat() in R/make_trim.R (line 260, column 5)
        cat() in R/make_trim.R (line 295, column 3)
        cat() in R/make_trim.R (line 296, column 3)
        cat() in R/map_rangetype.R (line 271, column 7)
        cat() in R/map_rangetype.R (line 286, column 7)
        cat() in R/map_rangetype.R (line 292, column 7)
        print() in R/map_rangetype.R (line 294, column 7)
        cat() in R/map_reanno.R (line 308, column 7)
        cat() in R/map_reanno.R (line 345, column 5)
        cat() in R/map_reanno.R (line 346, column 5)
        cat() in R/map_reanno.R (line 347, column 5)
        cat() in R/map_reanno.R (line 348, column 5)
        cat() in R/map_reanno.R (line 355, column 5)
        cat() in R/map_reanno.R (line 356, column 5)
        cat() in R/map_reanno.R (line 357, column 5)
        cat() in R/map_reanno.R (line 362, column 5)
        cat() in R/map_reanno.R (line 363, column 5)
        cat() in R/map_reanno.R (line 365, column 5)
        cat() in R/map_reanno.R (line 372, column 7)
        cat() in R/map_reanno.R (line 382, column 9)
        cat() in R/map_reanno.R (line 395, column 9)
        cat() in R/map_reanno.R (line 430, column 25)
        cat() in R/map_reanno.R (line 433, column 11)
        cat() in R/map_reanno.R (line 434, column 5)
        cat() in R/map_reanno.R (line 436, column 3)
        cat() in R/map_reanno.R (line 437, column 3)
        cat() in R/map_reanno.R (line 442, column 3)
        cat() in R/map_reanno.R (line 443, column 3)
        cat() in R/PAC_covplot.R (line 196, column 3)
        cat() in R/PAC_covplot.R (line 201, column 3)
        cat() in R/PAC_covplot.R (line 204, column 7)
        cat() in R/PAC_covplot.R (line 207, column 7)
        print() in R/PAC_covplot.R (line 208, column 7)
        print() in R/PAC_covplot.R (line 227, column 5)
        cat() in R/PAC_deseq.R (line 112, column 3)
        cat() in R/PAC_deseq.R (line 161, column 3)
        cat() in R/PAC_deseq.R (line 162, column 3)
        cat() in R/PAC_deseq.R (line 163, column 3)
        cat() in R/PAC_deseq.R (line 164, column 3)
        cat() in R/PAC_deseq.R (line 167, column 15)
        cat() in R/PAC_deseq.R (line 170, column 5)
        print() in R/PAC_deseq.R (line 172, column 5)
        print() in R/PAC_deseq.R (line 227, column 3)
        cat() in R/PAC_filter.R (line 133, column 7)
        cat() in R/PAC_filter.R (line 178, column 7)
        cat() in R/PAC_filter.R (line 206, column 7)
        cat() in R/PAC_filter.R (line 219, column 7)
        cat() in R/PAC_filter.R (line 222, column 7)
        cat() in R/PAC_filter.R (line 288, column 7)
        cat() in R/PAC_filter.R (line 300, column 7)
        print() in R/PAC_filter.R (line 286, column 7)
        cat() in R/PAC_gtf.R (line 146, column 3)
        cat() in R/PAC_gtf.R (line 196, column 7)
        cat() in R/PAC_gtf.R (line 203, column 9)
        cat() in R/PAC_gtf.R (line 275, column 3)
        cat() in R/PAC_gtf.R (line 300, column 3)
        cat() in R/PAC_gtf.R (line 316, column 7)
        cat() in R/PAC_gtf.R (line 327, column 7)
        cat() in R/PAC_gtf.R (line 328, column 7)
        cat() in R/PAC_gtf.R (line 338, column 3)
        cat() in R/PAC_gtf.R (line 389, column 5)
        cat() in R/PAC_gtf.R (line 435, column 5)
        cat() in R/PAC_gtf.R (line 439, column 7)
        cat() in R/PAC_gtf.R (line 451, column 5)
        cat() in R/PAC_gtf.R (line 455, column 7)
        cat() in R/PAC_mapper.R (line 168, column 5)
        cat() in R/PAC_mapper.R (line 172, column 7)
        cat() in R/PAC_mapper.R (line 176, column 9)
        cat() in R/PAC_mapper.R (line 222, column 5)
        cat() in R/PAC_mapper.R (line 228, column 7)
        cat() in R/PAC_mapper.R (line 229, column 7)
        print() in R/PAC_mapper.R (line 279, column 9)
        print() in R/PAC_mapper.R (line 288, column 9)
        cat() in R/PAC_nbias.R (line 149, column 4)
        print() in R/PAC_pca.R (line 221, column 3)
        print() in R/PAC_pie.R (line 256, column 5)
        cat() in R/PAC_saturation.R (line 71, column 3)
        cat() in R/PAC_saturation.R (line 80, column 3)
        cat() in R/PAC_saturation.R (line 82, column 3)
        cat() in R/PAC_saturation.R (line 84, column 3)
        cat() in R/PAC_saturation.R (line 122, column 3)
        cat() in R/PAC_trna.R (line 443, column 12)
        cat() in R/seqpac_generics_methods.R (line 366, column 3)
        cat() in R/seqpac_generics_methods.R (line 367, column 3)
        cat() in R/seqpac_generics_methods.R (line 368, column 3)
        cat() in R/seqpac_generics_methods.R (line 374, column 3)
        cat() in R/seqpac_generics_methods.R (line 375, column 3)
        cat() in R/seqpac_generics_methods.R (line 376, column 3)
        cat() in R/seqpac_generics_methods.R (line 378, column 5)
        cat() in R/seqpac_generics_methods.R (line 379, column 5)
        cat() in R/seqpac_generics_methods.R (line 382, column 5)
        cat() in R/seqpac_generics_methods.R (line 383, column 5)
        cat() in R/seqpac_S4classes.R (line 357, column 12)
        cat() in R/seqpac_S4classes.R (line 362, column 12)
        cat() in R/simplify_reanno.R (line 229, column 5)
        cat() in R/simplify_reanno.R (line 252, column 3)
        print() in R/simplify_reanno.R (line 266, column 3)
        cat() in R/tRNA_class.R (line 191, column 5)
    * NOTE: Avoid using '=' for assignment and use '<-' instead
      Found in files:
        R/make_counts.R (line 282, column 15)
        R/make_counts.R (line 518, column 13)
        R/PAC_mapper.R (line 362, column 18)
        R/PAC_mapper.R (line 363, column 20)
* Checking parsed R code in R directory, examples, vignettes...
    * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 5
      times)
        suppressWarnings() in R/make_counts.R (line 209, column 7)
        suppressWarnings() in R/make_cutadapt.R (line 146, column 5)
        suppressWarnings() in R/PAC_filter.R (line 260, column 7)
        suppressWarnings() in R/PAC_gtf.R (line 248, column 13)
        suppressWarnings() in R/PAC_gtf.R (line 405, column 17)
* Checking function lengths...
    * NOTE: Recommended function length <= 50 lines.
      There are 32 functions > 50 lines.
      The longest 5 functions are:
        make_trim() (R/make_trim.R, line 206): 530 lines
        make_counts() (R/make_counts.R, line 176): 404 lines
        PAC_trna() (R/PAC_trna.R, line 215): 377 lines
        PAC_gtf() (R/PAC_gtf.R, line 126): 372 lines
        add_reanno() (R/add_reanno.R, line 234): 279 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 multiples of 4 spaces for line indents, 4767
      lines(25%) are not.
    First 6 lines:
      R/add_reanno.R:235                        bio_perfect=FALSE, genome_max...
      R/add_reanno.R:237   if(isS4(reanno)){
      R/add_reanno.R:240   }else{
      R/add_reanno.R:242   }
      R/add_reanno.R:244   ## General setup ###############################
      R/add_reanno.R:245   stopifnot(any(do.call("c", lapply(reanno$Full_anno...
    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

[top]

merida1 Summary

[top]

Package: seqpac

Version: 0.99.5

RVersion: 4.2

BiocVersion: 3.15

BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data seqpac

BuildTime: 3 minutes 36.02 seconds

CheckCommand: BiocCheckGitClone('seqpac') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch seqpac_0.99.5.tar.gz && BiocCheck('seqpac_0.99.5.tar.gz', `new-package`=TRUE)

CheckTime: 14 minutes 59.95 seconds

BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh seqpac_0.99.5.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir

BuildBinTime: 0 minutes 11.24 seconds

PackageFileSize: 3741.67 KiB

BuildID:: seqpac_20220203141155

PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: seqpac. Starting Build package. Starting Check package. Starting Build package.

merida1 BUILD SRC output

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

 R CMD BUILD

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

* 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_0.99.5.tar.gz’

merida1 CHECK output

[top]

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

 BiocCheckGitClone('seqpac')

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

This is BiocCheckGitClone version 1.31.31. 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...
* Checking that provided CITATION file is correctly formatted...


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/2275/e11a97c319d683aaa2b181e34c4e4b77d31754a8/seqpac.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 ‘seqpac/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘seqpac’ version ‘0.99.5’
* 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 ‘seqpac’ can be installed ... [12s/12s] OK
* checking installed package size ... NOTE
  installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    extdata   3.4Mb
* 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 ... [16s/16s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [528s/439s] OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
make_counts     47.001  7.710  39.174
PAC_deseq       45.486  7.794  34.005
map_reanno      36.066  6.110  32.235
PAC_gtf         32.536  2.451  20.488
make_PAC        25.955  3.859  22.196
make_pheno      24.612  5.003  20.868
PAC_covplot     22.954  0.368  23.345
PAC_mapper      21.594  0.338  21.958
make_trim       21.050  0.378  21.429
make_cutadapt   19.832  0.426  20.257
add_reanno      16.214  2.263  16.909
simplify_reanno 11.808  1.848  12.063
reanno          11.367  1.814  11.594
as.reanno       10.443  1.740  10.637
names            9.104  1.835   9.335
overview         8.920  1.779   9.104
tRNA_class       8.647  1.820  10.080
full             8.570  1.701   8.696
PAC_trna         8.518  1.720   9.854
PAC_pca          7.617  0.082   7.713
PAC_nbias        7.188  0.021   7.212
make_reanno      5.926  1.123   6.013
PAC_jitter       6.569  0.143   6.729
map_rangetype    3.971  1.560   5.145
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ ERROR
TIMEOUT: R CMD check exceeded 14 mins






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

 BiocCheck('seqpac_0.99.5.tar.gz')

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

This is BiocCheck version 1.31.31. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
 [687s/382s]
 [688s/382s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
          ])))
      df[1, ] <- gsub("  ", " ", as.character(unlist(df[1, ])))
      if (!is.null(parse[[1]])) {
          file.remove(temp_out)
      }
      return(df)
  }`: task 1 failed - "error in running command"
  Backtrace:
      ▆
   1. ├─seqpac quiet(...) at test_PAC_generation.R:64:4
   2. │ └─base::force(x) at test_PAC_generation.R:12:4
   3. └─seqpac::make_counts(...)
   4.   └─seqpac::make_cutadapt(...)
   5.     └─... %dopar% ...
   6.       └─e$fun(obj, substitute(ex), parent.frame(), e$data)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 31 ]
  Error: Test failures
  In addition: Warning message:
  In .Internal(gc(verbose, reset, full)) :
    closing unused connection 3 (/Users/pkgbuild/packagebuilder/workers/jobs/2275/e11a97c319d683aaa2b181e34c4e4b77d31754a8/seqpac.Rcheck/seqpac/extdata/Stage3_Batch1_Inx13_S13.fastq.gz)
  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/e11a97c319d683aaa2b181e34c4e4b77d31754a8/seqpac.Rcheck/00check.log’
for details.

* Checking Package Dependencies...
Warning in system2(cmd, args, stdout = TRUE, stderr = FALSE, env = "R_DEFAULT_PACKAGES=NULL") :
  running command 'R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' -q --vanilla --slave -f /Library/Frameworks/R.framework/Versions/4.2/Resources/library/BiocCheck/script/checkBadDeps.R --args "/Users/pkgbuild/packagebuilder/workers/jobs/2275/e11a97c319d683aaa2b181e34c4e4b77d31754a8/seqpac_0.99.5.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpPMtgf0/file16d6c22e4e859/lib" 2>/dev/null' had status 1
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R Version dependency...
    * NOTE: Update R version dependency from 4.1.0 to 4.2.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
    Workflow
* 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 seqpac...
* Checking coding practice...
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
      Found in files:
        add_reanno.R (line 264, column 15)
        add_reanno.R (line 269, column 17)
        add_reanno.R (line 319, column 16)
        add_reanno.R (line 343, column 17)
        add_reanno.R (line 464, column 49)
        add_reanno.R (line 468, column 55)
        filtsep_bin.R (line 68, column 12)
        import_reanno.R (line 137, column 13)
        import_reanno.R (line 201, column 51)
        make_conv.R (line 157, column 12)
        make_conv.R (line 192, column 14)
        make_conv.R (line 229, column 12)
        make_conv.R (line 291, column 14)
        make_counts.R (line 357, column 35)
        make_counts.R (line 443, column 35)
        make_counts.R (line 510, column 40)
        make_cutadapt.R (line 172, column 37)
        make_pheno.R (line 199, column 16)
        make_pheno.R (line 206, column 16)
        make_reanno.R (line 168, column 16)
        make_reanno.R (line 170, column 12)
        make_reanno.R (line 221, column 14)
        make_reanno.R (line 226, column 18)
        make_reanno.R (line 253, column 15)
        make_trim.R (line 242, column 42)
        make_trim.R (line 300, column 7)
        make_trim.R (line 409, column 18)
        make_trim.R (line 619, column 53)
        make_trim.R (line 649, column 14)
        make_trim.R (line 662, column 12)
        map_rangetype.R (line 129, column 48)
        map_rangetype.R (line 152, column 14)
        map_rangetype.R (line 225, column 17)
        map_rangetype.R (line 312, column 14)
        map_rangetype.R (line 377, column 17)
        map_rangetype.R (line 383, column 17)
        map_reanno.R (line 361, column 12)
        map_reanno.R (line 371, column 15)
        merge_lanes.R (line 142, column 30)
        merge_lanes.R (line 150, column 14)
        PAC_check.R (line 118, column 52)
        PAC_check.R (line 127, column 54)
        PAC_covplot.R (line 219, column 14)
        PAC_covplot.R (line 238, column 14)
        PAC_covplot.R (line 262, column 12)
        PAC_covplot.R (line 268, column 36)
        PAC_covplot.R (line 272, column 30)
        PAC_covplot.R (line 280, column 54)
        PAC_covplot.R (line 301, column 12)
        PAC_deseq.R (line 125, column 13)
        PAC_filter.R (line 253, column 17)
        PAC_gtf.R (line 143, column 21)
        PAC_gtf.R (line 161, column 13)
        PAC_gtf.R (line 280, column 12)
        PAC_gtf.R (line 305, column 12)
        PAC_gtf.R (line 356, column 36)
        PAC_gtf.R (line 387, column 12)
        PAC_gtf.R (line 393, column 39)
        PAC_gtf.R (line 438, column 14)
        PAC_gtf.R (line 442, column 16)
        PAC_gtf.R (line 454, column 14)
        PAC_gtf.R (line 458, column 16)
        PAC_jitter.R (line 167, column 22)
        PAC_mapper.R (line 260, column 12)
        PAC_mapper.R (line 320, column 12)
        PAC_mapper.R (line 358, column 49)
        PAC_nbias.R (line 186, column 12)
        PAC_norm.R (line 61, column 15)
        PAC_pca.R (line 129, column 47)
        PAC_pie.R (line 167, column 15)
        PAC_pie.R (line 181, column 13)
        PAC_pie.R (line 193, column 24)
        PAC_pie.R (line 193, column 40)
        PAC_saturation.R (line 86, column 41)
        PAC_saturation.R (line 102, column 14)
        PAC_saturation.R (line 188, column 35)
        PAC_sizedist.R (line 174, column 14)
        PAC_sizedist.R (line 197, column 12)
        PAC_stackbar.R (line 153, column 15)
        PAC_stackbar.R (line 167, column 13)
        PAC_summary.R (line 144, column 50)
        PAC_trna.R (line 339, column 23)
        PAC_trna.R (line 359, column 16)
        simplify_reanno.R (line 202, column 23)
        simplify_reanno.R (line 264, column 15)
        simplify_reanno.R (line 282, column 12)
    * NOTE: Avoid 'cat' and 'print' outside of 'show' methods
      Found in files:
        cat() in R/add_reanno.R (line 250, column 3)
        cat() in R/add_reanno.R (line 253, column 5)
        cat() in R/add_reanno.R (line 261, column 5)
        cat() in R/add_reanno.R (line 281, column 9)
        cat() in R/add_reanno.R (line 313, column 5)
        cat() in R/add_reanno.R (line 333, column 5)
        cat() in R/add_reanno.R (line 386, column 13)
        cat() in R/add_reanno.R (line 425, column 9)
        cat() in R/add_reanno.R (line 436, column 5)
        cat() in R/add_reanno.R (line 485, column 5)
        cat() in R/import_reanno.R (line 130, column 3)
        cat() in R/import_reanno.R (line 138, column 5)
        cat() in R/import_reanno.R (line 178, column 9)
        cat() in R/import_reanno.R (line 186, column 9)
        cat() in R/import_reanno.R (line 245, column 5)
        cat() in R/make_conv.R (line 121, column 3)
        cat() in R/make_conv.R (line 132, column 3)
        cat() in R/make_conv.R (line 143, column 7)
        cat() in R/make_conv.R (line 155, column 3)
        cat() in R/make_conv.R (line 190, column 5)
        cat() in R/make_conv.R (line 225, column 3)
        cat() in R/make_conv.R (line 305, column 3)
        cat() in R/make_counts.R (line 183, column 3)
        cat() in R/make_counts.R (line 196, column 5)
        cat() in R/make_counts.R (line 198, column 5)
        cat() in R/make_counts.R (line 200, column 3)
        cat() in R/make_counts.R (line 219, column 5)
        cat() in R/make_counts.R (line 220, column 5)
        cat() in R/make_counts.R (line 221, column 5)
        cat() in R/make_counts.R (line 222, column 5)
        cat() in R/make_counts.R (line 239, column 7)
        cat() in R/make_counts.R (line 240, column 7)
        cat() in R/make_counts.R (line 241, column 7)
        cat() in R/make_counts.R (line 243, column 7)
        cat() in R/make_counts.R (line 244, column 7)
        cat() in R/make_counts.R (line 246, column 7)
        cat() in R/make_counts.R (line 268, column 5)
        cat() in R/make_counts.R (line 269, column 5)
        cat() in R/make_counts.R (line 270, column 5)
        cat() in R/make_counts.R (line 271, column 5)
        cat() in R/make_counts.R (line 290, column 7)
        cat() in R/make_counts.R (line 291, column 7)
        cat() in R/make_counts.R (line 292, column 7)
        cat() in R/make_counts.R (line 293, column 7)
        cat() in R/make_counts.R (line 295, column 7)
        cat() in R/make_counts.R (line 296, column 7)
        cat() in R/make_counts.R (line 298, column 7)
        cat() in R/make_counts.R (line 299, column 7)
        cat() in R/make_counts.R (line 301, column 7)
        cat() in R/make_counts.R (line 302, column 7)
        cat() in R/make_counts.R (line 304, column 7)
        cat() in R/make_counts.R (line 341, column 3)
        cat() in R/make_counts.R (line 378, column 3)
        cat() in R/make_counts.R (line 410, column 5)
        cat() in R/make_counts.R (line 427, column 5)
        cat() in R/make_counts.R (line 431, column 7)
        cat() in R/make_counts.R (line 433, column 7)
        cat() in R/make_counts.R (line 470, column 3)
        print() in R/make_counts.R (line 201, column 3)
        print() in R/make_counts.R (line 242, column 7)
        print() in R/make_counts.R (line 245, column 7)
        print() in R/make_counts.R (line 294, column 7)
        print() in R/make_counts.R (line 297, column 7)
        print() in R/make_counts.R (line 300, column 7)
        print() in R/make_counts.R (line 303, column 7)
        print() in R/make_counts.R (line 568, column 5)
        cat() in R/make_cutadapt.R (line 135, column 3)
        cat() in R/make_cutadapt.R (line 136, column 3)
        cat() in R/make_pheno.R (line 221, column 5)
        cat() in R/make_pheno.R (line 226, column 7)
        cat() in R/make_pheno.R (line 228, column 5)
        cat() in R/make_pheno.R (line 236, column 5)
        cat() in R/make_pheno.R (line 256, column 5)
        cat() in R/make_pheno.R (line 261, column 3)
        print() in R/make_pheno.R (line 229, column 5)
        cat() in R/make_reanno.R (line 181, column 3)
        cat() in R/make_reanno.R (line 239, column 3)
        cat() in R/make_reanno.R (line 272, column 5)
        cat() in R/make_reanno.R (line 292, column 7)
        cat() in R/make_reanno.R (line 296, column 7)
        cat() in R/make_reanno.R (line 298, column 7)
        cat() in R/make_reanno.R (line 306, column 7)
        cat() in R/make_trim.R (line 225, column 5)
        cat() in R/make_trim.R (line 230, column 7)
        cat() in R/make_trim.R (line 234, column 5)
        cat() in R/make_trim.R (line 244, column 5)
        cat() in R/make_trim.R (line 260, column 5)
        cat() in R/make_trim.R (line 295, column 3)
        cat() in R/make_trim.R (line 296, column 3)
        cat() in R/map_rangetype.R (line 271, column 7)
        cat() in R/map_rangetype.R (line 286, column 7)
        cat() in R/map_rangetype.R (line 292, column 7)
        print() in R/map_rangetype.R (line 294, column 7)
        cat() in R/map_reanno.R (line 308, column 7)
        cat() in R/map_reanno.R (line 345, column 5)
        cat() in R/map_reanno.R (line 346, column 5)
        cat() in R/map_reanno.R (line 347, column 5)
        cat() in R/map_reanno.R (line 348, column 5)
        cat() in R/map_reanno.R (line 355, column 5)
        cat() in R/map_reanno.R (line 356, column 5)
        cat() in R/map_reanno.R (line 357, column 5)
        cat() in R/map_reanno.R (line 362, column 5)
        cat() in R/map_reanno.R (line 363, column 5)
        cat() in R/map_reanno.R (line 365, column 5)
        cat() in R/map_reanno.R (line 372, column 7)
        cat() in R/map_reanno.R (line 382, column 9)
        cat() in R/map_reanno.R (line 395, column 9)
        cat() in R/map_reanno.R (line 430, column 25)
        cat() in R/map_reanno.R (line 433, column 11)
        cat() in R/map_reanno.R (line 434, column 5)
        cat() in R/map_reanno.R (line 436, column 3)
        cat() in R/map_reanno.R (line 437, column 3)
        cat() in R/map_reanno.R (line 442, column 3)
        cat() in R/map_reanno.R (line 443, column 3)
        cat() in R/PAC_covplot.R (line 196, column 3)
        cat() in R/PAC_covplot.R (line 201, column 3)
        cat() in R/PAC_covplot.R (line 204, column 7)
        cat() in R/PAC_covplot.R (line 207, column 7)
        print() in R/PAC_covplot.R (line 208, column 7)
        print() in R/PAC_covplot.R (line 227, column 5)
        cat() in R/PAC_deseq.R (line 112, column 3)
        cat() in R/PAC_deseq.R (line 161, column 3)
        cat() in R/PAC_deseq.R (line 162, column 3)
        cat() in R/PAC_deseq.R (line 163, column 3)
        cat() in R/PAC_deseq.R (line 164, column 3)
        cat() in R/PAC_deseq.R (line 167, column 15)
        cat() in R/PAC_deseq.R (line 170, column 5)
        print() in R/PAC_deseq.R (line 172, column 5)
        print() in R/PAC_deseq.R (line 227, column 3)
        cat() in R/PAC_filter.R (line 133, column 7)
        cat() in R/PAC_filter.R (line 178, column 7)
        cat() in R/PAC_filter.R (line 206, column 7)
        cat() in R/PAC_filter.R (line 219, column 7)
        cat() in R/PAC_filter.R (line 222, column 7)
        cat() in R/PAC_filter.R (line 288, column 7)
        cat() in R/PAC_filter.R (line 300, column 7)
        print() in R/PAC_filter.R (line 286, column 7)
        cat() in R/PAC_gtf.R (line 146, column 3)
        cat() in R/PAC_gtf.R (line 196, column 7)
        cat() in R/PAC_gtf.R (line 203, column 9)
        cat() in R/PAC_gtf.R (line 275, column 3)
        cat() in R/PAC_gtf.R (line 300, column 3)
        cat() in R/PAC_gtf.R (line 316, column 7)
        cat() in R/PAC_gtf.R (line 327, column 7)
        cat() in R/PAC_gtf.R (line 328, column 7)
        cat() in R/PAC_gtf.R (line 338, column 3)
        cat() in R/PAC_gtf.R (line 389, column 5)
        cat() in R/PAC_gtf.R (line 435, column 5)
        cat() in R/PAC_gtf.R (line 439, column 7)
        cat() in R/PAC_gtf.R (line 451, column 5)
        cat() in R/PAC_gtf.R (line 455, column 7)
        cat() in R/PAC_mapper.R (line 168, column 5)
        cat() in R/PAC_mapper.R (line 172, column 7)
        cat() in R/PAC_mapper.R (line 176, column 9)
        cat() in R/PAC_mapper.R (line 222, column 5)
        cat() in R/PAC_mapper.R (line 228, column 7)
        cat() in R/PAC_mapper.R (line 229, column 7)
        print() in R/PAC_mapper.R (line 279, column 9)
        print() in R/PAC_mapper.R (line 288, column 9)
        cat() in R/PAC_nbias.R (line 149, column 4)
        print() in R/PAC_pca.R (line 221, column 3)
        print() in R/PAC_pie.R (line 256, column 5)
        cat() in R/PAC_saturation.R (line 71, column 3)
        cat() in R/PAC_saturation.R (line 80, column 3)
        cat() in R/PAC_saturation.R (line 82, column 3)
        cat() in R/PAC_saturation.R (line 84, column 3)
        cat() in R/PAC_saturation.R (line 122, column 3)
        cat() in R/PAC_trna.R (line 443, column 12)
        cat() in R/seqpac_generics_methods.R (line 366, column 3)
        cat() in R/seqpac_generics_methods.R (line 367, column 3)
        cat() in R/seqpac_generics_methods.R (line 368, column 3)
        cat() in R/seqpac_generics_methods.R (line 374, column 3)
        cat() in R/seqpac_generics_methods.R (line 375, column 3)
        cat() in R/seqpac_generics_methods.R (line 376, column 3)
        cat() in R/seqpac_generics_methods.R (line 378, column 5)
        cat() in R/seqpac_generics_methods.R (line 379, column 5)
        cat() in R/seqpac_generics_methods.R (line 382, column 5)
        cat() in R/seqpac_generics_methods.R (line 383, column 5)
        cat() in R/seqpac_S4classes.R (line 357, column 12)
        cat() in R/seqpac_S4classes.R (line 362, column 12)
        cat() in R/simplify_reanno.R (line 229, column 5)
        cat() in R/simplify_reanno.R (line 252, column 3)
        print() in R/simplify_reanno.R (line 266, column 3)
        cat() in R/tRNA_class.R (line 191, column 5)
    * NOTE: Avoid using '=' for assignment and use '<-' instead
      Found in files:
        R/make_counts.R (line 282, column 15)
        R/make_counts.R (line 518, column 13)
        R/PAC_mapper.R (line 362, column 18)
        R/PAC_mapper.R (line 363, column 20)
* Checking parsed R code in R directory, examples, vignettes...
    * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 5
      times)
        suppressWarnings() in R/make_counts.R (line 209, column 7)
        suppressWarnings() in R/make_cutadapt.R (line 146, column 5)
        suppressWarnings() in R/PAC_filter.R (line 260, column 7)
        suppressWarnings() in R/PAC_gtf.R (line 248, column 13)
        suppressWarnings() in R/PAC_gtf.R (line 405, column 17)
* Checking function lengths...
    * NOTE: Recommended function length <= 50 lines.
      There are 32 functions > 50 lines.
      The longest 5 functions are:
        make_trim() (R/make_trim.R, line 206): 530 lines
        make_counts() (R/make_counts.R, line 176): 404 lines
        PAC_trna() (R/PAC_trna.R, line 215): 377 lines
        PAC_gtf() (R/PAC_gtf.R, line 126): 372 lines
        add_reanno() (R/add_reanno.R, line 234): 279 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 multiples of 4 spaces for line indents, 4767
      lines(25%) are not.
    First 6 lines:
      R/add_reanno.R:235                        bio_perfect=FALSE, genome_max...
      R/add_reanno.R:237   if(isS4(reanno)){
      R/add_reanno.R:240   }else{
      R/add_reanno.R:242   }
      R/add_reanno.R:244   ## General setup ###############################
      R/add_reanno.R:245   stopifnot(any(do.call("c", lapply(reanno$Full_anno...
    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

merida1 BUILD BIN output

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

 R CMD BUILD

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

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir seqpac_0.99.5.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)