Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘single/DESCRIPTION’ ... OK
* preparing ‘single’:
* 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
* building ‘single_0.99.18.tar.gz’

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 BiocCheckGitClone('single')

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This is BiocCheckGitClone version 1.31.36. 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




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 R CMD CHECK

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* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2528/26226515bdbc0945af4f35b91159abca2cacbeec/single.Rcheck’
* using R Under development (unstable) (2022-03-02 r81842)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘single/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘single’ version ‘0.99.18’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘single’ can be installed ... [37s/38s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [48s/49s] NOTE
pileup_by_QUAL: no visible binding for global variable ‘count.y’
pileup_by_QUAL: no visible binding for global variable ‘count.x’
pileup_by_QUAL: no visible binding for global variable ‘nucleotide’
pileup_by_QUAL: no visible binding for global variable ‘QUAL’
single_consensus_byBarcode: no visible binding for global variable
  ‘BCid’
Undefined global functions or variables:
  BCid QUAL count.x count.y nucleotide
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [114s/144s] OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
fit_logregr                26.825  0.415  36.694
single_train               26.882  0.311  34.082
p_prior_errors              8.336  0.131   9.142
p_prior_mutations           8.219  0.113   9.082
pileup_by_QUAL              8.070  0.110   9.266
single_consensus_byBarcode  4.575  0.049   6.101
single_evaluate             3.955  0.032   5.055
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/2528/26226515bdbc0945af4f35b91159abca2cacbeec/single.Rcheck/00check.log’
for details.






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 BiocCheck('single_0.99.18.tar.gz')

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This is BiocCheck version 1.31.36. 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 '/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/2528/26226515bdbc0945af4f35b91159abca2cacbeec/single_0.99.18.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpGLc3os/file91af3651089c/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...
    * NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or
      removed
* 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 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 single...
* Checking coding practice...
    * NOTE: Avoid sapply(); use vapply()
      Found in files:
        R/single_consensus_byBarcode.r (line 59, column 21)
        R/single_evaluate.r (line 156, column 23)
    * NOTE: Avoid 'cat' and 'print' outside of 'show' methods
      Found in files:
        print() in R/evaluate_fits.r (line 52, column 17)
        cat() in R/fit_logregr.r (line 91, column 17)
        cat() in R/single_train.r (line 73, column 17)
        cat() in R/single_train.r (line 75, column 17)
        cat() in R/single_train.r (line 80, column 17)
        cat() in R/single_train.r (line 85, column 17)
        cat() in R/single_train.r (line 92, column 17)
        cat() in R/single_train.r (line 101, column 17)
    * NOTE: Avoid using '=' for assignment and use '<-' instead
      Found in files:
        R/evaluate_fits.r (line 29, column 18)
        R/evaluate_fits.r (line 41, column 19)
        R/fit_logregr.r (line 35, column 18)
        R/fit_logregr.r (line 92, column 19)
        R/pileup_by_QUAL.R (line 22, column 10)
        R/pileup_by_QUAL.R (line 62, column 13)
        R/single_consensus_byBarcode.r (line 50, column 14)
        R/single_consensus_byBarcode.r (line 62, column 22)
        R/single_evaluate.r (line 52, column 37)
        R/single_evaluate.r (line 53, column 33)
        R/single_evaluate.r (line 61, column 16)
        R/single_evaluate.r (line 63, column 16)
        R/single_evaluate.r (line 85, column 14)
        R/single_evaluate.r (line 87, column 12)
        R/single_evaluate.r (line 90, column 24)
        R/single_evaluate.r (line 97, column 26)
        R/single_evaluate.r (line 104, column 25)
        R/single_evaluate.r (line 105, column 25)
        R/single_evaluate.r (line 110, column 23)
        R/single_evaluate.r (line 111, column 24)
        R/single_evaluate.r (line 115, column 14)
        R/single_evaluate.r (line 117, column 18)
        R/single_evaluate.r (line 119, column 17)
        R/single_train.r (line 55, column 21)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
    * NOTE: Recommended function length <= 50 lines.
      There are 3 functions > 50 lines.
      The longest 5 functions are:
        single_evaluate() (R/single_evaluate.r, line 45): 120 lines
        fit_logregr() (R/fit_logregr.r, line 32): 96 lines
        single_train() (R/single_train.r, line 37): 73 lines
        pileup_by_QUAL() (R/pileup_by_QUAL.R, line 20): 49 lines
        single_consensus_byBarcode() (R/single_consensus_byBarcode.r,
      line 31): 40 lines
* Checking man page documentation...
* Checking package NEWS...
    * NOTE: Consider adding a NEWS file, so your package news will be
      included in Bioconductor release announcements.
* 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; 135 lines (9%) are > 80 characters
      long.
    First 6 lines:
      R/data.R:9 #' Mutational rate matrix for error-prone PCR, obtained from...
      R/evaluate_fits.r:7 #' @param data_fits Data.frame with columns positio...
      R/fit_logregr.r:3 #' This is an auxiliary function in single package. I...
      R/fit_logregr.r:4 #' @param counts_pnq Data frame with columns position...
      R/fit_logregr.r:6 #' @param p_prior_errors Data frame with columns posi...
      R/fit_logregr.r:7 #' @param p_prior_mutations Data frame with columns w...
    * NOTE: Consider multiples of 4 spaces for line indents, 91
      lines(6%) are not.
    First 6 lines:
      man/evaluate_fits.Rd:8   pos_range,
      man/evaluate_fits.Rd:9   q_range,
      man/evaluate_fits.Rd:10   output_file,
      man/evaluate_fits.Rd:11   data_fits,
      man/evaluate_fits.Rd:12   ref_seq,
      man/evaluate_fits.Rd:13   verbose = FALSE,
    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: 10
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

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 R CMD BUILD

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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir single_0.99.18.tar.gz'
>>>>>>> 

* installing *source* package ‘single’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (single)