===============================
R CMD BUILD
===============================
* checking for file ‘turboGliph/DESCRIPTION’ ... OK
* preparing ‘turboGliph’:
* 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 ‘turboGliph_0.99.1.tar.gz’
===============================
BiocCheckGitClone('turboGliph')
===============================
This is BiocCheckGitClone version 1.29.10. 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
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2185/42bb77d47096e801b129a47fc5c8a2353c2e51a6/turboGliph.Rcheck’
* using R version 4.1.0 beta (2021-05-03 r80259)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘turboGliph/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘turboGliph’ version ‘0.99.1’
* 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 ‘turboGliph’ can be installed ... [6s/6s] 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 ... [8s/8s] 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 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 ... [19s/19s] OK
* 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: OK
===============================
BiocCheck('turboGliph_0.99.1.tar.gz')
===============================
This is BiocCheck version 1.29.10. 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...
* 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...
* 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 turboGliph...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...................
* NOTE: Recommended function length <= 50 lines.
There are 8 functions > 50 lines.
The longest 5 functions are:
gliph_combined() (R/gliph_combined.R, line 239): 1460 lines
gliph2() (R/gliph2.R, line 163): 1203 lines
turbo_gliph() (R/turbo_gliph_function_foreach.R, line 172): 989
lines
plot_network() (R/plot_network.R, line 58): 655 lines
de_novo_TCRs() (R/de_novo_tcrs.R, line 79): 493 lines
* Checking man page documentation...
* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
load_gliph_output.Rd
* Checking package NEWS...
* 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; 2216 lines (27%) are > 80
characters long.
First 6 lines:
R/data.R:4 #' another list with a data frame containing the sequences a...
R/data.R:8 #' \item "gliph_reference": Reference database of 162,165 CD...
R/data.R:9 # \item "human_v1.0_CD4": Reference database of 889,808 CDR3...
R/data.R:10 # \item "human_v1.0_CD8": Reference database of 336,510 CDR...
R/data.R:11 # \item "human_v1.0_CD48": Reference database of 1,226,318 ...
R/data.R:12 # \item "human_v2.0_CD4": Reference database of 772,312 CDR...
* NOTE: Consider 4 spaces instead of tabs; 13 lines (0%) contain
tabs.
First 6 lines:
R/gliph_combined.R:776 base::colnames(motifs_df) <- base::c("moti...
R/gliph_combined.R:1091 base::colnames(structs_df) <- base::c("st...
R/turbo_gliph_function_foreach.R:699 part_2_res <- base::matrix(nco...
vignettes/Introduction-to-turboGliph.Rmd:169 * *clonal.expansion.score*...
vignettes/Introduction-to-turboGliph.Rmd:302 * *vgene.score* : score fo...
vignettes/Introduction-to-turboGliph.Rmd:303 * *clonal.expansion.score*...
* NOTE: Consider multiples of 4 spaces for line indents, 3650
lines(44%) are not.
First 6 lines:
R/de_novo_tcrs.R:80 result_folder = "",
R/de_novo_tcrs.R:81 clustering_output = NULL,
R/de_novo_tcrs.R:82 refdb_beta = "gliph_refere...
R/de_novo_tcrs.R:83 normalization = FALSE,
R/de_novo_tcrs.R:84 accept_sequences_with_C_F_...
R/de_novo_tcrs.R:85 sims = 100000,
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