merida1 Summary
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Package: COTAN |
Version: 0.99.10 |
RVersion: 4.2
|
BiocVersion: 3.15
|
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data COTAN |
BuildTime: 2 minutes 48.55 seconds |
CheckCommand: BiocCheckGitClone('COTAN') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch COTAN_0.99.10.tar.gz && BiocCheck('COTAN_0.99.10.tar.gz', `new-package`=TRUE) |
CheckTime: 3 minutes 19.72 seconds |
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh COTAN_0.99.10.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
BuildBinTime: 0 minutes 17.40 seconds |
PackageFileSize: 4449.76 KiB |
BuildID:: COTAN_20211226095554 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: COTAN. Starting Build package. Starting Check package. Starting Build package. |
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 0. Build Package status: 0. |
merida1 BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘COTAN/DESCRIPTION’ ... OK
* preparing ‘COTAN’:
* 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 ‘COTAN_0.99.10.tar.gz’
merida1 CHECK output
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===============================
BiocCheckGitClone('COTAN')
===============================
This is BiocCheckGitClone version 1.31.19. 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/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2151/27234e7a79944604aaa843ccb62bb66e5124d963/COTAN.Rcheck’
* using R Under development (unstable) (2021-11-01 r81125)
* using platform: x86_64-apple-darwin17.0 (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 ‘0.99.10’
* 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 ... [17s/17s] 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/15s] 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 ... [51s/41s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
automatic.COTAN.object.creation 30.249 1.362 25.980
clean 5.464 0.169 0.863
* 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’ [47s/33s]
[47s/34s] 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
‘/Users/pkgbuild/packagebuilder/workers/jobs/2151/27234e7a79944604aaa843ccb62bb66e5124d963/COTAN.Rcheck/00check.log’
for details.
===============================
BiocCheck('COTAN_0.99.10.tar.gz')
===============================
This is BiocCheck version 1.31.19. 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...
* 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 using '=' for assignment and use '<-' instead
Found in files:
= in R/COTAN_main.R (line 266, column 24)
= in R/COTAN_main.R (line 515, column 28)
= in R/internal_functions.R (line 5, column 25)
= in R/internal_functions.R (line 215, column 20)
= in R/internal_functions.R (line 243, column 32)
= in R/internal_functions.R (line 245, column 26)
* 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:
_anonymous_.503() (R/COTAN_main.R, line 503): 132 lines
_anonymous_.1072() (R/COTAN_main.R, line 1072): 128 lines
_anonymous_.680() (R/COTAN_main.R, line 680): 124 lines
_anonymous_.118() (R/COTAN_main.R, line 118): 121 lines
_anonymous_.261() (R/COTAN_main.R, line 261): 65 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; 297 lines (9%) are > 80 characters
long.
First 6 lines:
R/COTAN_main.R:38 #' @param object the dataframe containing the raw dat...
R/COTAN_main.R:123 ...
R/COTAN_main.R:126 ...
R/COTAN_main.R:127 axis.text.y = ele...
R/COTAN_main.R:130 ...
R/COTAN_main.R:132 ...
* NOTE: Consider multiples of 4 spaces for line indents, 993
lines(29%) 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:77 }
R/COTAN_main.R:118 function(object) {
R/COTAN_main.R:120 mycolours <- c("A" = "#8491B4B2","B...
R/COTAN_main.R:122 my_theme <- theme(axis.text.x = el...
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: 5
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
merida1 BUILD BIN output
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===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir COTAN_0.99.10.tar.gz'
>>>>>>>
* installing *source* package ‘COTAN’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (COTAN)
nebbiolo1 Summary
[top]
Package: COTAN |
Version: 0.99.10 |
RVersion: 4.2
|
BiocVersion: 3.15
|
BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data COTAN |
BuildTime: 1 minutes 56.58 seconds |
CheckCommand: BiocCheckGitClone('COTAN') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings COTAN_0.99.10.tar.gz && BiocCheck('COTAN_0.99.10.tar.gz', `new-package`=TRUE) |
CheckTime: 2 minutes 10.94 seconds |
BuildBinCommand: |
BuildBinTime: |
PackageFileSize: 4445.40 KiB |
BuildID:: COTAN_20211226095554 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: COTAN. Starting Build package. Starting Check package. |
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 0. |
nebbiolo1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘COTAN/DESCRIPTION’ ... OK
* preparing ‘COTAN’:
* 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 ‘COTAN_0.99.10.tar.gz’
nebbiolo1 CHECK output
[top]
===============================
BiocCheckGitClone('COTAN')
===============================
This is BiocCheckGitClone version 1.31.19. 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/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2151/27234e7a79944604aaa843ccb62bb66e5124d963/COTAN.Rcheck’
* using R Under development (unstable) (2021-11-10 r81171)
* 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 ‘0.99.10’
* 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 ... [10s/10s] 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] [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 ... [46s/31s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
automatic.COTAN.object.creation 20.049 8.988 18.833
clean 1.664 3.939 0.661
* 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’ [41s/25s]
[42s/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/2151/27234e7a79944604aaa843ccb62bb66e5124d963/COTAN.Rcheck/00check.log’
for details.
===============================
BiocCheck('COTAN_0.99.10.tar.gz')
===============================
This is BiocCheck version 1.31.19. 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...
* 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 using '=' for assignment and use '<-' instead
Found in files:
= in R/COTAN_main.R (line 266, column 24)
= in R/COTAN_main.R (line 515, column 28)
= in R/internal_functions.R (line 5, column 25)
= in R/internal_functions.R (line 215, column 20)
= in R/internal_functions.R (line 243, column 32)
= in R/internal_functions.R (line 245, column 26)
* 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:
_anonymous_.503() (R/COTAN_main.R, line 503): 132 lines
_anonymous_.1072() (R/COTAN_main.R, line 1072): 128 lines
_anonymous_.680() (R/COTAN_main.R, line 680): 124 lines
_anonymous_.118() (R/COTAN_main.R, line 118): 121 lines
_anonymous_.261() (R/COTAN_main.R, line 261): 65 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; 297 lines (9%) are > 80 characters
long.
First 6 lines:
R/COTAN_main.R:38 #' @param object the dataframe containing the raw dat...
R/COTAN_main.R:123 ...
R/COTAN_main.R:126 ...
R/COTAN_main.R:127 axis.text.y = ele...
R/COTAN_main.R:130 ...
R/COTAN_main.R:132 ...
* NOTE: Consider multiples of 4 spaces for line indents, 993
lines(29%) 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:77 }
R/COTAN_main.R:118 function(object) {
R/COTAN_main.R:120 mycolours <- c("A" = "#8491B4B2","B...
R/COTAN_main.R:122 my_theme <- theme(axis.text.x = el...
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: 5
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
nebbiolo1 BUILD BIN output
[top]