merida1 Summary
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| Package: mbOmic |
| Version: 0.99.12 |
| RVersion: 4.2
|
| BiocVersion: 3.15
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data mbOmic |
| BuildTime: 0 minutes 46.73 seconds |
| CheckCommand: BiocCheckGitClone('mbOmic') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch mbOmic_0.99.12.tar.gz && BiocCheck('mbOmic_0.99.12.tar.gz', `new-package`=TRUE) |
| CheckTime: 3 minutes 8.04 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh mbOmic_0.99.12.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 19.97 seconds |
| PackageFileSize: 296.55 KiB |
| BuildID:: mbOmic_20220204160812 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: mbOmic. 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 ‘mbOmic/DESCRIPTION’ ... OK
* preparing ‘mbOmic’:
* 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
* building ‘mbOmic_0.99.12.tar.gz’
merida1 CHECK output
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===============================
BiocCheckGitClone('mbOmic')
===============================
This is BiocCheckGitClone version 1.31.31. 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/2234/dc913a420ee3f910d5240abbd16363f879f52692/mbOmic.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mbOmic/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mbOmic’ version ‘0.99.12’
* 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 ‘mbOmic’ can be installed ... [20s/20s] 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 ... [19s/19s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [36s/36s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plot_network 7.732 0.420 8.153
coExpress 7.521 0.353 7.874
plot_coExpress 5.046 0.004 5.050
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [6s/6s]
[6s/6s] 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('mbOmic_0.99.12.tar.gz')
===============================
This is BiocCheck version 1.31.31. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
Warning in system2(cmd, args, stdout = TRUE, stderr = FALSE, env = "R_DEFAULT_PACKAGES=NULL") :
running command 'R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' -q --vanilla --slave -f /Library/Frameworks/R.framework/Versions/4.2/Resources/library/BiocCheck/script/checkBadDeps.R --args "/Users/pkgbuild/packagebuilder/workers/jobs/2234/dc913a420ee3f910d5240abbd16363f879f52692/mbOmic_0.99.12.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpWSvbGs/filee5a44e972057/lib" 2>/dev/null' had status 1
* 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 4.1.0 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 mbOmic...
* Checking coding practice...
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
print() in R/plot.R (line 88, column 25)
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid '<<-' if possible (found 4 times)
<<- in R/enterotype.R (line 104, column 32)
<<- in R/enterotype.R (line 105, column 30)
<<- in R/enterotype.R (line 106, column 36)
<<- in R/enterotype.R (line 107, column 36)
* Checking function lengths...
* 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; 109 lines (5%) are > 80 characters
long.
First 6 lines:
R/AllClasses.R:30 msg <- c(msg, "Samples and F...
R/AllClasses.R:34 msg <- c(msg, "Dimension of ...
R/AllClasses.R:56 #' m.path <- system.file("extdata", "metabolites_and_...
R/AllClasses.R:79 #' b.path <- system.file("extdata", "metabolites_and_...
R/enterotype.R:5 #' \sqrt{0.5 \times KLD (P||\frac{P + Q}{2}) + 0...
R/enterotype.R:24 sqrt(0.5 * KLD(x, (x + y) / 2...
* NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain
tabs.
First 1 lines:
R/m-corr.R:73 registerDoParallel(cores = ncore)
* NOTE: Consider multiples of 4 spaces for line indents, 149
lines(7%) are not.
First 6 lines:
R/AllClasses.R:16 representation = representation(Samples = 'c...
R/AllClasses.R:17 Features = "...
R/AllClasses.R:18 dt = "data.t...
R/AllClasses.R:19 'VIRTUAL'),
R/AllClasses.R:20 validity = function (object) {
R/AllClasses.R:21 Sam <- unique(object@Samples)
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/3.15/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 mbOmic_0.99.12.tar.gz'
>>>>>>>
* installing *source* package ‘mbOmic’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘nrow’ from package ‘base’ in package ‘mbOmic’
Creating a generic function for ‘ncol’ from package ‘base’ in package ‘mbOmic’
** 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 (mbOmic)
nebbiolo1 Summary
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| Package: mbOmic |
| Version: 0.99.12 |
| RVersion: 4.2
|
| BiocVersion: 3.15
|
| BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data mbOmic |
| BuildTime: 0 minutes 27.82 seconds |
| CheckCommand: BiocCheckGitClone('mbOmic') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings mbOmic_0.99.12.tar.gz && BiocCheck('mbOmic_0.99.12.tar.gz', `new-package`=TRUE) |
| CheckTime: 2 minutes 10.32 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 289.40 KiB |
| BuildID:: mbOmic_20220204160812 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: mbOmic. 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 ‘mbOmic/DESCRIPTION’ ... OK
* preparing ‘mbOmic’:
* 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
* building ‘mbOmic_0.99.12.tar.gz’
nebbiolo1 CHECK output
[top]
===============================
BiocCheckGitClone('mbOmic')
===============================
This is BiocCheckGitClone version 1.31.31. 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/2234/dc913a420ee3f910d5240abbd16363f879f52692/mbOmic.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 ‘mbOmic/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mbOmic’ version ‘0.99.12’
* 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 ‘mbOmic’ can be installed ... [13s/13s] 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 ... [13s/13s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [29s/29s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plot_network 6.497 0.092 6.534
coExpress 6.335 0.115 6.394
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [4s/4s]
[4s/4s] 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('mbOmic_0.99.12.tar.gz')
===============================
This is BiocCheck version 1.31.31. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
Warning in system2(cmd, args, stdout = TRUE, stderr = FALSE, env = "R_DEFAULT_PACKAGES=NULL") :
running command 'R_DEFAULT_PACKAGES=NULL '/home/biocbuild/bbs-3.15-bioc/R/bin/R' -q --vanilla --slave -f /home/biocbuild/bbs-3.15-bioc/R/library/BiocCheck/script/checkBadDeps.R --args "/home/pkgbuild/packagebuilder/workers/jobs/2234/dc913a420ee3f910d5240abbd16363f879f52692/mbOmic_0.99.12.tar.gz" "/tmp/RtmpDljeYd/file186799343cb5e3/lib" 2>/dev/null' had status 1
* 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 4.1.0 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 mbOmic...
* Checking coding practice...
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
print() in R/plot.R (line 88, column 25)
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid '<<-' if possible (found 4 times)
<<- in R/enterotype.R (line 104, column 32)
<<- in R/enterotype.R (line 105, column 30)
<<- in R/enterotype.R (line 106, column 36)
<<- in R/enterotype.R (line 107, column 36)
* Checking function lengths...
* 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; 109 lines (5%) are > 80 characters
long.
First 6 lines:
R/AllClasses.R:30 msg <- c(msg, "Samples and F...
R/AllClasses.R:34 msg <- c(msg, "Dimension of ...
R/AllClasses.R:56 #' m.path <- system.file("extdata", "metabolites_and_...
R/AllClasses.R:79 #' b.path <- system.file("extdata", "metabolites_and_...
R/enterotype.R:5 #' \sqrt{0.5 \times KLD (P||\frac{P + Q}{2}) + 0...
R/enterotype.R:24 sqrt(0.5 * KLD(x, (x + y) / 2...
* NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain
tabs.
First 1 lines:
R/m-corr.R:73 registerDoParallel(cores = ncore)
* NOTE: Consider multiples of 4 spaces for line indents, 149
lines(7%) are not.
First 6 lines:
R/AllClasses.R:16 representation = representation(Samples = 'c...
R/AllClasses.R:17 Features = "...
R/AllClasses.R:18 dt = "data.t...
R/AllClasses.R:19 'VIRTUAL'),
R/AllClasses.R:20 validity = function (object) {
R/AllClasses.R:21 Sam <- unique(object@Samples)
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/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
nebbiolo1 BUILD BIN output
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