===============================
R CMD BUILD
===============================
* checking for file ‘tinytools/DESCRIPTION’ ... OK
* preparing ‘tinytools’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
-----------------------------------
ERROR: dependencies ‘tidyr’, ‘ggplot2’, ‘plotly’, ‘pbapply’, ‘clisymbols’, ‘plyr’, ‘readxl’, ‘rvest’, ‘leaflet’ are not available for package ‘tinytools’
* removing ‘/private/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T/Rtmpbwq3K5/Rinst10024d248451/tinytools’
-----------------------------------
ERROR: package installation failed
===============================
BiocCheckGitClone('tinytools')
===============================
This is BiocCheckGitClone version 1.31.21. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* ERROR: System Files found that should not be git tracked:
tinytools.Rproj
.DS_Store
docs/.DS_Store
inst/.DS_Store
inst/rmarkdown/.DS_Store
inst/rmarkdown/templates/.DS_Store
inst/rmarkdown/templates/massqc/.DS_Store
inst/rmarkdown/templates/massqc/skeleton/.DS_Store
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
Summary:
ERROR count: 1
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
BiocCheckGitClone FAILED.
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2470/tinytools_20220106190213/tinytools.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘tinytools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘tinytools’ 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 ... WARNING
Found the following file with a non-portable file name:
man/trans_ID (1).Rd
These are not fully portable file names.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘tinytools’ can be installed ... [4s/4s] 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 ... [4s/4s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... WARNING
Rd files with duplicated name 'trans_ID':
‘trans_ID (1).Rd’ ‘trans_ID.Rd’
Rd files with duplicated alias 'trans_ID':
‘trans_ID (1).Rd’ ‘trans_ID.Rd’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [1s/6s] ERROR
Running examples in ‘tinytools-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_compound_class
> ### Title: get_compound_class
> ### Aliases: get_compound_class
>
> ### ** Examples
>
> get_compound_class()
✔ QZDWODWEESGPLC-UHFFFAOYSA-N is available in website.
Warning in is_string(right) : restarting interrupted promise evaluation
Error in utils::packageVersion("metflow2") :
there is no package called ‘metflow2’
Calls: <Anonymous> ... <Anonymous> -> stopifnot -> is_string -> paste0 -> <Anonymous>
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [1s/1s]
[1s/1s] 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: 1 ERROR, 2 WARNINGs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2470/tinytools_20220106190213/tinytools.Rcheck/00check.log’
for details.
===============================
BiocCheck('tinytools_0.99.1.tar.gz')
===============================
This is BiocCheck version 1.31.21. 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 4.1 to 4.2.0.
* 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 for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
vignettes/contact_us.Rmd
vignettes/tinytools.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of tinytools...
* Checking coding practice...
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
cat() in R/read_mgf.R (line 11, column 5)
cat() in R/setwd_project.R (line 51, column 13)
cat() in R/setwd_project.R (line 59, column 13)
cat() in R/setwd_project.R (line 69, column 9)
cat() in R/tinytools_logo.R (line 31, column 5)
cat() in R/tinytools_logo.R (line 32, column 5)
cat() in R/tinytools_logo.R (line 33, column 5)
cat() in R/tinytools_logo.R (line 36, column 5)
cat() in R/trans_ID.R (line 141, column 13)
cat() in R/trans_ID.R (line 281, column 9)
cat() in R/trans_ID.R (line 288, column 9)
cat() in R/trans_ID.R (line 331, column 9)
* WARNING: Avoid class membership checks with class() / is() and ==
/ !=; Use is(x, 'class') for S4 classes
Found in files:
classyfire.R (line 19, column 30)
classyfire.R (line 30, column 30)
classyfire.R (line 39, column 30)
classyfire.R (line 78, column 37)
classyfire.R (line 139, column 37)
classyfire.R (line 146, column 43)
classyfire.R (line 158, column 35)
classyfire.R (line 164, column 44)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 13 functions > 50 lines.
The longest 5 functions are:
ms2_plot() (R/ms2_plot.R, line 57): 213 lines
get_compound_class() (R/classyfire.R, line 12): 166 lines
trans_ID() (R/trans_ID.R, line 30): 163 lines
trans_id_database() (R/trans_ID.R, line 206): 134 lines
split_formula() (R/adduct_formula.R, line 123): 113 lines
* Checking man page documentation...
* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
read_mgf.Rd, setwd_project.Rd, setwd_win.Rd, trans_ID (1).Rd
* Checking package NEWS...
* NOTE: Consider adding a NEWS file, so your package news will be
included in Bioconductor release announcements.
* 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; 81 lines (2%) are > 80 characters
long.
First 6 lines:
R/long_wide_convertor.R:1 #' ##----------------------------------------...
R/long_wide_convertor.R:37 #' ##---------------------------------------...
R/long_wide_convertor.R:38 #' ##---------------------------------------...
R/ms_format_converter.R:3 #' #' Conversion of MS analysis files between...
R/ms_format_converter.R:5 #' #' @param algorithm Either \code{"pwiz"} (...
R/ms_format_converter.R:6 #' #' ProteoWizard), \code{"openms"} (imple...
* NOTE: Consider multiples of 4 spaces for line indents, 183
lines(5%) are not.
First 6 lines:
R/adduct_formula.R:18 adduct = "M-H2O+H") {
R/adduct_formula.R:211 any(is.na(x))
R/adduct_formula.R:212 }), ]
R/attach.R:12 dirname(getNamespaceInfo(pkg, "path"))
R/attach.R:13 }
R/attach.R:28 return(invisible())
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: 1
NOTE count: 8
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