===============================
BiocCheckGitClone('OptiLCMS')
===============================
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...
* Checking that provided CITATION file is correctly formatted...
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/2210/27df33313de6d1432575817f227ea73aa544c567/OptiLCMS.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 ‘OptiLCMS/DESCRIPTION’ ... OK
* this is package ‘OptiLCMS’ version ‘0.99.2’
* 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 ‘OptiLCMS’ can be installed ... [32s/32s] OK
* checking installed package size ... NOTE
installed size is 6.8Mb
sub-directories of 1Mb or more:
doc 2.2Mb
libs 3.1Mb
* 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 ... [31s/31s] 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [113s/95s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
PerformPeakProfiling 74.962 4.63 62.192
* 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: 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2210/27df33313de6d1432575817f227ea73aa544c567/OptiLCMS.Rcheck/00check.log’
for details.
===============================
BiocCheck('OptiLCMS_0.99.2.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...
* NOTE: Update R version dependency from 4.0.0 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...
* 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 OptiLCMS...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
Found in files:
Optimize_params.R (line 452, column 25)
Optimize_params.R (line 457, column 24)
Optimize_params.R (line 462, column 25)
Optimize_params.R (line 467, column 24)
Optimize_params.R (line 472, column 32)
Optimize_params.R (line 836, column 7)
Optimize_params.R (line 1337, column 15)
Optimize_params.R (line 1370, column 18)
Optimize_params.R (line 1862, column 11)
Optimize_params.R (line 1930, column 21)
Other_Utils.R (line 96, column 5)
Other_Utils.R (line 105, column 17)
Other_Utils.R (line 112, column 17)
Other_Utils.R (line 119, column 15)
Other_Utils.R (line 135, column 5)
Perform_functions.R (line 961, column 18)
Perform_functions.R (line 1105, column 13)
Perform_functions.R (line 1136, column 13)
Perform_functions.R (line 1565, column 9)
Resume_functions.R (line 913, column 9)
Resume_functions.R (line 1236, column 28)
Resume_functions.R (line 1248, column 28)
Resume_functions.R (line 1260, column 28)
Resume_functions.R (line 1272, column 28)
Resume_functions.R (line 1284, column 28)
Resume_functions.R (line 1296, column 28)
Resume_functions.R (line 1327, column 28)
Resume_functions.R (line 1339, column 28)
Resume_functions.R (line 1351, column 28)
Resume_functions.R (line 1363, column 28)
ROI_Extraction.R (line 117, column 23)
ROI_Extraction.R (line 128, column 23)
ROI_Extraction.R (line 198, column 15)
ROI_Extraction.R (line 209, column 26)
ROI_Extraction.R (line 233, column 17)
ROI_Extraction.R (line 254, column 15)
ROI_Extraction.R (line 267, column 15)
ROI_Extraction.R (line 347, column 11)
ROI_Extraction.R (line 545, column 27)
ROI_Extraction.R (line 582, column 21)
ROI_Extraction.R (line 588, column 28)
ROI_Extraction.R (line 646, column 16)
ROI_Extraction.R (line 659, column 11)
ROI_Extraction.R (line 668, column 30)
ROI_Extraction.R (line 671, column 30)
ROI_Extraction.R (line 756, column 11)
ROI_Extraction.R (line 775, column 7)
ROI_Extraction.R (line 784, column 23)
ROI_Extraction.R (line 842, column 18)
ROI_Extraction.R (line 864, column 18)
ROI_Extraction.R (line 964, column 22)
Spectra_import.R (line 744, column 11)
Spectra_import.R (line 792, column 26)
Spectra_import.R (line 797, column 37)
Spectra_import.R (line 959, column 26)
Spectra_import.R (line 964, column 37)
Spectra_import.R (line 1097, column 32)
Spectra_import.R (line 1108, column 34)
Spectra_import.R (line 1119, column 27)
Spectra_import.R (line 1244, column 12)
Spectra_import.R (line 1310, column 12)
Spectra_import.R (line 1312, column 19)
Spectra_import.R (line 1320, column 30)
Spectra_import.R (line 1454, column 10)
Spectra_import.R (line 1479, column 12)
Spectra_Utils.R (line 401, column 15)
Spectra_Utils.R (line 2431, column 18)
Spectra_Utils.R (line 2842, column 11)
Spectra_Utils.R (line 3231, column 19)
Spectra_Utils.R (line 3354, column 15)
Spectra_Utils.R (line 3386, column 15)
Spectra_Utils.R (line 3670, column 38)
Spectra_Utils.R (line 3758, column 12)
Spectra_Utils.R (line 3772, column 15)
Spectra_Utils.R (line 3780, column 15)
Spectra_Utils.R (line 3807, column 16)
Spectra_Utils.R (line 4317, column 30)
Spectra_Utils.R (line 4631, column 13)
Spectra_Utils.R (line 4691, column 18)
Spectra_Utils.R (line 4841, column 19)
Spectra_Utils.R (line 4881, column 40)
Spectra_Utils.R (line 4909, column 22)
Spectra_Utils.R (line 5034, column 3)
Spectra_Utils.R (line 5061, column 14)
Spectra_Utils.R (line 5083, column 18)
Spectra_Utils.R (line 5154, column 14)
Spectra_Utils.R (line 5163, column 16)
Spectra_Utils.R (line 5168, column 16)
Spectra_Utils.R (line 5194, column 13)
Spectra_Utils.R (line 5408, column 14)
Spectra_Utils.R (line 5527, column 24)
Spectra_Utils.R (line 6507, column 18)
Spectra_Utils.R (line 6512, column 26)
Spectra_visulization.R (line 375, column 7)
Spectra_visulization.R (line 627, column 13)
Spectra_visulization.R (line 628, column 25)
Spectra_visulization.R (line 799, column 7)
Spectra_visulization.R (line 830, column 23)
Spectra_visulization.R (line 1286, column 7)
Warning in readLines(infile) :
incomplete final line found on '/tmp/Rtmp824EUs/file2a541d1235e8d6/OptiLCMS/inst/script/Example_Running_Script.R'
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid '<<-' if possible (found 26 times)
<<- in
/tmp/Rtmp824EUs/file2a541d1235e8d6/OptiLCMS/R/Optimize_params.R
(line 54, column 14)
<<- in
/tmp/Rtmp824EUs/file2a541d1235e8d6/OptiLCMS/R/Params_db.R (line
81, column 14)
<<- in
/tmp/Rtmp824EUs/file2a541d1235e8d6/OptiLCMS/R/Perform_functions.R
(line 96, column 16)
<<- in
/tmp/Rtmp824EUs/file2a541d1235e8d6/OptiLCMS/R/Resume_functions.R
(line 25, column 14)
<<- in
/tmp/Rtmp824EUs/file2a541d1235e8d6/OptiLCMS/R/Resume_functions.R
(line 514, column 14)
<<- in
/tmp/Rtmp824EUs/file2a541d1235e8d6/OptiLCMS/R/Resume_functions.R
(line 542, column 14)
<<- in
/tmp/Rtmp824EUs/file2a541d1235e8d6/OptiLCMS/R/Resume_functions.R
(line 1040, column 14)
<<- in
/tmp/Rtmp824EUs/file2a541d1235e8d6/OptiLCMS/R/Resume_functions.R
(line 1088, column 14)
<<- in
/tmp/Rtmp824EUs/file2a541d1235e8d6/OptiLCMS/R/Resume_functions.R
(line 1132, column 14)
<<- in
/tmp/Rtmp824EUs/file2a541d1235e8d6/OptiLCMS/R/Resume_functions.R
(line 1153, column 14)
<<- in
/tmp/Rtmp824EUs/file2a541d1235e8d6/OptiLCMS/R/ROI_Extraction.R
(line 103, column 16)
<<- in
/tmp/Rtmp824EUs/file2a541d1235e8d6/OptiLCMS/R/Spectra_import.R
(line 117, column 16)
<<- in
/tmp/Rtmp824EUs/file2a541d1235e8d6/OptiLCMS/R/Spectra_Utils.R
(line 42, column 14)
<<- in
/tmp/Rtmp824EUs/file2a541d1235e8d6/OptiLCMS/R/Spectra_Utils.R
(line 1079, column 14)
<<- in
/tmp/Rtmp824EUs/file2a541d1235e8d6/OptiLCMS/R/Spectra_Utils.R
(line 1299, column 14)
<<- in
/tmp/Rtmp824EUs/file2a541d1235e8d6/OptiLCMS/R/Spectra_Utils.R
(line 1399, column 14)
<<- in
/tmp/Rtmp824EUs/file2a541d1235e8d6/OptiLCMS/R/Spectra_Utils.R
(line 1518, column 14)
<<- in
/tmp/Rtmp824EUs/file2a541d1235e8d6/OptiLCMS/R/Spectra_Utils.R
(line 1660, column 16)
<<- in
/tmp/Rtmp824EUs/file2a541d1235e8d6/OptiLCMS/R/Spectra_Utils.R
(line 1878, column 14)
<<- in
/tmp/Rtmp824EUs/file2a541d1235e8d6/OptiLCMS/R/Spectra_Utils.R
(line 2203, column 14)
<<- in
/tmp/Rtmp824EUs/file2a541d1235e8d6/OptiLCMS/R/Spectra_Utils.R
(line 2656, column 14)
<<- in
/tmp/Rtmp824EUs/file2a541d1235e8d6/OptiLCMS/R/Spectra_Utils.R
(line 4353, column 14)
<<- in
/tmp/Rtmp824EUs/file2a541d1235e8d6/OptiLCMS/R/Spectra_Utils.R
(line 4843, column 20)
<<- in
/tmp/Rtmp824EUs/file2a541d1235e8d6/OptiLCMS/R/Spectra_Utils.R
(line 4849, column 23)
<<- in
/tmp/Rtmp824EUs/file2a541d1235e8d6/OptiLCMS/R/Spectra_Utils.R
(line 5037, column 16)
<<- in
/tmp/Rtmp824EUs/file2a541d1235e8d6/OptiLCMS/R/Spectra_Utils.R
(line 5037, column 24)
* Checking function lengths..................................................
* NOTE: Recommended function length <= 50 lines.
There are 90 functions > 50 lines.
The longest 5 functions are:
SetPeakParam() (R/Params_db.R, line 67): 2008 lines
PerformPeakAnnotation() (R/Perform_functions.R, line 531): 873
lines
PeakPicking_centWave_slave() (R/Spectra_Utils.R, line 154): 482
lines
PerformROIExtraction() (R/ROI_Extraction.R, line 89): 422 lines
PlotXIC() (R/Spectra_visulization.R, line 320): 419 lines
* Checking man page documentation...
* 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; 1478 lines (6%) are > 80 characters
long.
First 6 lines:
R/Global_setting.R:181 #' @return void function, return nothing but wil...
R/Optimize_params.R:18 #' @param running.controller The resuming pipeli...
R/Optimize_params.R:31 #' DataFiles <- dir(system.file("mzData", packag...
R/Optimize_params.R:36 #' # best_params <- PerformParamsOptimization(mS...
R/Optimize_params.R:186 param[["ppm"]] <- param[["ppm"]]; # E...
R/Optimize_params.R:192 param[["prefilter"]] <- 3; # Estimati...
* NOTE: Consider multiples of 4 spaces for line indents, 10990
lines(47%) are not.
First 6 lines:
R/C_function.R:22 function(y, threshold, num, istart = 1) {
R/C_function.R:24 y <- as.double(y)
R/C_function.R:26 if (.C(
R/C_function.R:34 )$n > 0)
R/C_function.R:36 else
R/C_function.R:39 }
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: 7
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