Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘GenProSeq/DESCRIPTION’ ... OK
* preparing ‘GenProSeq’:
* 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
* looking to see if a ‘data/datalist’ file should be added
  NB: this package now depends on R (>= 3.5.0)
  WARNING: Added dependency on R >= 3.5.0 because serialized objects in
  serialize/load version 3 cannot be read in older versions of R.
  File(s) containing such objects:
    ‘GenProSeq/data/example_PTEN.rda’ ‘GenProSeq/data/example_luxA.rda’
* building ‘GenProSeq_0.99.19.tar.gz’

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 BiocCheckGitClone('GenProSeq')

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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...
* 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/2304/27df19a3a44f2acef97da0601ac5b9e4361a97c6/GenProSeq.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 ‘GenProSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GenProSeq’ version ‘0.99.19’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GenProSeq’ can be installed ... [14s/14s] 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 ... [16s/16s] NOTE
fit_VAE: no visible binding for global variable ‘z_mean’
fit_VAE: no visible binding for global variable ‘z_log_stddev’
fit_VAE : vae_loss: no visible binding for global variable
  ‘z_log_stddev’
fit_VAE : vae_loss: no visible binding for global variable ‘z_mean’
layer_embedding_token_position : <anonymous>: no visible global
  function definition for ‘super’
layer_embedding_token_position : <anonymous>: no visible binding for
  global variable ‘self’
layer_transformer_encoder : <anonymous>: no visible global function
  definition for ‘super’
layer_transformer_encoder : <anonymous>: no visible binding for global
  variable ‘self’
Undefined global functions or variables:
  self super z_log_stddev z_mean

Found the following assignments to the global environment:
File ‘GenProSeq/R/VAE.R’:
  assign("z_mean", layer_dense(encoded, latent_dim, name = "z_mean"), 
    envir = globalenv())
  assign("z_log_stddev", layer_dense(encoded, latent_dim, name = "z_log_stddev"), 
    envir = globalenv())
File ‘GenProSeq/R/transformer.R’:
  assign("maxlen", maxlen, envir = globalenv())
  assign("vocab_size", vocab_size, envir = globalenv())
  assign("embed_dim", embed_dim, envir = globalenv())
  assign("embed_dim", embed_dim, envir = globalenv())
  assign("num_heads", num_heads, envir = globalenv())
  assign("ff_dim", ff_dim, envir = globalenv())
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [159s/143s] OK
Examples with CPU (user + system) or elapsed time > 5s
      user system elapsed
VAE 60.893  3.606  56.800
ART 55.280  4.128  54.818
GAN 24.988  1.883  22.893
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [13s/12s]
 [13s/12s] OK
* checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' imports not declared from:
  ‘VAExprs’ ‘ggseqlogo’ ‘stringdist’
* 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: 3 NOTEs
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/2304/27df19a3a44f2acef97da0601ac5b9e4361a97c6/GenProSeq.Rcheck/00check.log’
for details.






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 BiocCheck('GenProSeq_0.99.19.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...
    * NOTE: Consider clarifying how 8 object(s) are initialized. Maybe
      they are part of a data set loaded with data(), or perhaps part
      of an object referenced in with() or within().
    function (object)
      fit_VAE (z_mean)
      fit_VAE (z_log_stddev)
      fit_VAE  (z_log_stddev)
      fit_VAE  (z_mean)
      layer_embedding_token_position  (super)
      layer_embedding_token_position  (self)
      layer_transformer_encoder  (super)
      layer_transformer_encoder  (self)
* 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 3.5.0 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...
    * NOTE: Consider adding these automatically suggested biocViews:
      ATACSeq, Preprocessing, Network
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...
* 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 GenProSeq...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths    * NOTE: Recommended function length <= 50 lines.
      There are 6 functions > 50 lines.
      The longest 5 functions are:
        fit_GAN() (R/GAN.R, line 1): 390 lines
        fit_VAE() (R/VAE.R, line 1): 276 lines
        fit_ART() (R/ART.R, line 1): 171 lines
        layer_transformer_encoder() (R/transformer.R, line 48): 105
      lines
        gen_VAE() (R/VAE.R, line 282): 84 lines
* Checking man page documentation...
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
  and vignette source...
    * NOTE: Consider shorter lines; 163 lines (6%) are > 80 characters
      long.
    First 6 lines:
      R/ART.R:45             stop("the embedding dimension is a multiple of t...
      R/ART.R:52                 stop("the embedding dimension is a multiple ...
      R/ART.R:56             result$preprocessing$removed_prot_seq <- checked...
      R/ART.R:59             seq_encode_pad <- DeepPINCS::get_seq_encode_pad(...
      R/ART.R:63                 temp <- rbind(temp, embed(rev(seq_encode_pad...
      R/ART.R:72                 result$preprocessing$removed_prot_seq_val <-...
    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: 5
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 GenProSeq_0.99.19.tar.gz'
>>>>>>> 

* installing *source* package ‘GenProSeq’ ...
** using staged installation
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GenProSeq)