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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
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_0.99.2.tar.gz’
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BiocCheckGitClone('GenProSeq')
===============================
This is BiocCheckGitClone version 1.29.14. 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/3.14/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
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R CMD CHECK
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* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2304/3d2e39e56e82c431e555fe46627e8dacab281507/GenProSeq.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (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 ‘0.99.2’
* 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 ‘GenProSeq’ can be installed ... [14s/9s] 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 ... [15s/11s] 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [103s/64s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
ART 31.871 11.913 27.309
VAE 32.930 4.733 22.396
GAN 13.457 1.507 8.809
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [25s/11s]
[25s/11s] 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: 2 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2304/3d2e39e56e82c431e555fe46627e8dacab281507/GenProSeq.Rcheck/00check.log’
for details.
===============================
BiocCheck('GenProSeq_0.99.2.tar.gz')
===============================
This is BiocCheck version 1.29.14. 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...
* 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 3.5.0 to 4.1.0.
* 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 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; 151 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: 6
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.14/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output