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
* building ‘GenProSeq_0.99.21.tar.gz’

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 BiocCheckGitClone('GenProSeq')

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This is BiocCheckGitClone version 1.31.28. 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/2304/9456fd1e9e198c3a11bbda0fe3fdf1d8ae0b2407/GenProSeq.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 ‘GenProSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GenProSeq’ version ‘0.99.21’
* 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 ... [20s/20s] 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 ... [22s/22s] 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/1s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [166s/156s] ERROR
Running examples in ‘GenProSeq-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: VAE
> ### Title: Variational autoencoder for generating protein sequences
> ### Aliases: fit_VAE gen_VAE
> 
> ### ** Examples
> 
> if (keras::is_keras_available() & reticulate::py_available()) {
+     data("example_luxA")
+     label <- substr(example_luxA, 3, 3)
+     
+     # model parameters
+     length_seq <- 360
+     embedding_dim <- 8
+     batch_size <- 128
+     epochs <- 2
+     
+     # CVAE
+     VAE_result <- fit_VAE(prot_seq = example_luxA,
+                         label = label,
+                         length_seq = length_seq,
+                         embedding_dim = embedding_dim,
+                         embedding_args = list(iter = 20),
+                         intermediate_encoder_layers = list(layer_dense(units = 128),
+                                                             layer_dense(units = 16)),
+                         intermediate_decoder_layers = list(layer_dense(units = 16),
+                                                             layer_dense(units = 128)),
+                         prot_seq_val = example_luxA,
+                         label_val = label,
+                         epochs = epochs,
+                         batch_size = batch_size,
+                         use_generator = FALSE,
+                         optimizer = keras::optimizer_adam(clipnorm = 0.1),
+                         callbacks = keras::callback_early_stopping(
+                             monitor = "val_loss",
+                             patience = 10,
+                             restore_best_weights = TRUE))
+     gen_prot_VAE_I <- gen_VAE(VAE_result, label = rep("I", 100), num_seq = 100)
+     gen_prot_VAE_L <- gen_VAE(VAE_result, label = rep("L", 100), num_seq = 100)
+     
+     
+     ### from preprocessing
+     VAE_result2 <- fit_VAE(intermediate_encoder_layers = list(layer_dense(units = 128),
+                                                             layer_dense(units = 16)),
+                             intermediate_decoder_layers = list(layer_dense(units = 16),
+                                                             layer_dense(units = 128)),
+                             epochs = epochs, batch_size = batch_size,
+                             preprocessing = VAE_result$preprocessing,
+                             use_generator = FALSE,
+                             optimizer = keras::optimizer_adam(clipnorm = 0.1),
+                             callbacks = keras::callback_early_stopping(
+                                 monitor = "val_loss",
+                                 patience = 10,
+                                 restore_best_weights = TRUE))
+     gen_prot_VAE2_I <- gen_VAE(VAE_result2, label = rep("I", 100), num_seq = 100)
+     gen_prot_VAE2_L <- gen_VAE(VAE_result2, label = rep("L", 100), num_seq = 100)
+ }
pre-processing...
training...
Train on 2283 samples, validate on 2283 samples
Epoch 1/2

 128/2283 [>.............................] - ETA: 0s - loss: 115148.1953
 640/2283 [=======>......................] - ETA: 0s - loss: 27811.6139 
1152/2283 [==============>...............] - ETA: 0s - loss: 16502.1927
1664/2283 [====================>.........] - ETA: 0s - loss: 11929.7007
2176/2283 [===========================>..] - ETA: 0s - loss: 9557.3785 
2283/2283 [==============================] - 0s 216us/sample - loss: 9219.1388 - val_loss: 1576.5574
Epoch 2/2

 128/2283 [>.............................] - ETA: 0s - loss: 1582.9139
 640/2283 [=======>......................] - ETA: 0s - loss: 1404.3431
1152/2283 [==============>...............] - ETA: 0s - loss: 1359.6810
1664/2283 [====================>.........] - ETA: 0s - loss: 1307.0357
2048/2283 [=========================>....] - ETA: 0s - loss: 1300.4870
2283/2283 [==============================] - 0s 191us/sample - loss: 1297.2103 - val_loss: 1196.2888
generating...
post-processing...
generating...
post-processing...
Error in fit_VAE(intermediate_encoder_layers = list(layer_dense(units = 128),  : 
  check number of sequences for train in the preprocessed result
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [13s/13s]
 [14s/14s] OK
* checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' imports not declared from:
  ‘VAExprs’ ‘ggseqlogo’ ‘stringdist’
* checking package vignettes in ‘inst/doc’ ... OK
* checking runni* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 3 NOTEs
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/2304/9456fd1e9e198c3a11bbda0fe3fdf1d8ae0b2407/GenProSeq.Rcheck/00check.log’
for details.





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 BiocCheck('GenProSeq_0.99.21.tar.gz')

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This is BiocCheck version 1.31.28. 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/2304/9456fd1e9e198c3a11bbda0fe3fdf1d8ae0b2407/GenProSeq_0.99.21.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpRAfUpl/file499204e9ddb/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...
* 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...
    * NOTE: Avoid 'cat' and 'print' outside of 'show' methods
      Found in files:
        cat() in R/GAN.R (line 222, column 9)
        cat() in R/GAN.R (line 370, column 9)
        cat() in R/GAN.R (line 372, column 13)
        cat() in R/GAN.R (line 374, column 9)
        cat() in R/GAN.R (line 376, column 13)
        cat() in R/GAN.R (line 378, column 9)
* 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): 395 lines
        fit_VAE() (R/VAE.R, line 1): 281 lines
        fit_ART() (R/ART.R, line 1): 177 lines
        layer_transformer_encoder() (R/transformer.R, line 48): 105
      lines
        gen_VAE() (R/VAE.R, line 287): 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; 187 lines (7%) are > 80 characters
      long.
    First 6 lines:
      R/ART.R:37         if (is.null(x_train)) stop("check embedded sequence ...
      R/ART.R:40         if (is.null(y_train)) stop("check labels for train i...
      R/ART.R:43         if (is.null(length_seq)) stop("check length of seque...
      R/ART.R:45         if (is.null(embedding_dim)) stop("check dimension of...
      R/ART.R:47         if (is.null(lenc)) stop("check encoded labels in the...
      R/ART.R:49         if (is.null(num_AA)) stop("check number of amino aci...
    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: 4
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_0.99.21.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)