===============================
BiocCheckGitClone('COTAN')
===============================
This is BiocCheckGitClone version 1.29.8. 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/2151/cd6bda73f7991fb8b7886e8747b10c7248cde328/COTAN.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 ‘COTAN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘COTAN’ version ‘0.99.5’
* 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 ... 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 ‘COTAN’ can be installed ... [11s/11s] 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 ... [9s/9s] NOTE
automatic.COTAN.object.creation,data.frame: no visible binding for
global variable ‘means’
automatic.COTAN.object.creation,data.frame: no visible binding for
global variable ‘PC1’
automatic.COTAN.object.creation,data.frame: no visible binding for
global variable ‘PC2’
automatic.COTAN.object.creation,data.frame: no visible binding for
global variable ‘nu’
clean,scCOTAN: no visible binding for global variable ‘PC1’
clean,scCOTAN: no visible binding for global variable ‘PC2’
fun_linear,scCOTAN : <anonymous>: no visible global function definition
for ‘python_PCA’
plot_GDI,scCOTAN: no visible binding for global variable ‘sum.raw.norm’
plot_heatmap,ANY: no visible binding for global variable ‘time’
plot_heatmap,ANY: no visible binding for global variable ‘g2’
Undefined global functions or variables:
PC1 PC2 g2 means nu python_PCA sum.raw.norm time
Consider adding
importFrom("stats", "time")
to your NAMESPACE file.
* 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 R/sysdata.rda ... OK
* checking line endings in shell scripts ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [44s/27s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
automatic.COTAN.object.creation 20.449 9.364 18.904
clean 1.732 5.268 0.651
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘spelling.R’ [0s/0s]
Comparing ‘spelling.Rout’ to ‘spelling.Rout.save’ ...6c6
< NULL
---
> All Done!
Running ‘testthat.R’ [44s/25s]
[44s/25s] 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: 2 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2151/cd6bda73f7991fb8b7886e8747b10c7248cde328/COTAN.Rcheck/00check.log’
for details.
===============================
BiocCheck('COTAN_0.99.5.tar.gz')
===============================
This is BiocCheck version 1.29.8. 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 COTAN...
* Checking coding practice...
* NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
COTAN_main.R (line 70, column 31)
COTAN_main.R (line 71, column 31)
COTAN_main.R (line 74, column 31)
COTAN_main.R (line 213, column 25)
COTAN_main.R (line 930, column 38)
COTAN_main.R (line 997, column 37)
COTAN_main.R (line 1222, column 60)
internal_functions.R (line 201, column 50)
* NOTE: Avoid the use of 'paste' in condition signals
Found in files:
/tmp/RtmpnoLMdO/file51b12740a8edd/COTAN/R/COTAN_main.R (line
1384, column 24)
/tmp/RtmpnoLMdO/file51b12740a8edd/COTAN/R/internal_functions.R
(line 343, column 24)
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
/tmp/RtmpnoLMdO/file51b12740a8edd/COTAN/R/COTAN_main.R (line
433, column 28)
/tmp/RtmpnoLMdO/file51b12740a8edd/COTAN/R/COTAN_main.R (line
1360, column 24)
/tmp/RtmpnoLMdO/file51b12740a8edd/COTAN/R/COTAN_main.R (line
1384, column 30)
/tmp/RtmpnoLMdO/file51b12740a8edd/COTAN/R/internal_functions.R
(line 343, column 30)
* Checking parsed R code in R directory, examples, vignettes...
Found @ in man/get.expected.ct.Rd
Found @ in man/get.gene.coexpression.space.Rd
Found @ in man/get.observed.ct.Rd
Found @ in vignettes/Guided_tutorial.Rmd
* NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* Checking function lengths...................
* NOTE: Recommended function length <= 50 lines.
There are 10 functions > 50 lines.
The longest 5 functions are:
_anonymous_.520() (R/COTAN_main.R, line 520): 152 lines
_anonymous_.715() (R/COTAN_main.R, line 715): 135 lines
_anonymous_.1135() (R/COTAN_main.R, line 1135): 134 lines
_anonymous_.120() (R/COTAN_main.R, line 120): 122 lines
_anonymous_.884() (R/COTAN_main.R, line 884): 72 lines
* Checking man page documentation...
* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
plot_general.heatmap.Rd, plot_heatmap.Rd
* NOTE: Usage of dontrun{} / donttest{} found in man page examples.
11% of man pages use one of these cases.
Found in the following files:
plot_general.heatmap.Rd
plot_heatmap.Rd
* NOTE: Use donttest{} instead of dontrun{}.
Found in the following files:
plot_general.heatmap.Rd
plot_heatmap.Rd
* 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; 317 lines (11%) are > 80 characters
long.
First 6 lines:
R/COTAN_main.R:38 #' @param object the dataframe containing the raw dat...
R/COTAN_main.R:125 ...
R/COTAN_main.R:128 ...
R/COTAN_main.R:129 axis.text.y = ele...
R/COTAN_main.R:132 ...
R/COTAN_main.R:134 ...
* NOTE: Consider multiples of 4 spaces for line indents, 1062
lines(35%) are not.
First 6 lines:
R/COTAN_main.R:62 is.null(attr(object@raw, "class")) ){
R/COTAN_main.R:64 "sparseM...
R/COTAN_main.R:76 #object@clusters = rep(NA,ncol(object@r...
R/COTAN_main.R:77 #names(object@clusters)=colnames(object...
R/COTAN_main.R:79 }
R/COTAN_main.R:120 function(object) {
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/3.14/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output