nebbiolo1 Summary
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Package: EpiMix.data |
Version: 0.99.0 |
RVersion: 4.2
|
BiocVersion: 3.15
|
BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data EpiMix.data |
BuildTime: 0 minutes 0.44 seconds |
CheckCommand: BiocCheckGitClone('EpiMix.data') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings EpiMix.data_0.99.0.tar.gz && BiocCheck('EpiMix.data_0.99.0.tar.gz', `new-package`=TRUE) |
CheckTime: 1 minutes 30.87 seconds |
BuildBinCommand: |
BuildBinTime: |
PackageFileSize: 1845.44 KiB |
BuildID:: EpiMix.data_20220405141730 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: EpiMix.data. Starting Build package. Starting Check package. |
PostProcessing: Finished Git clone. Package type: ExperimentData. Installing dependency status: 0. Checking git clone status: 1. Installing package status: 0. Build Package status: 0. Checking Package status: 1. |
nebbiolo1 BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘EpiMix.data/DESCRIPTION’ ... OK
* preparing ‘EpiMix.data’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
NB: this package now depends on R (>= 3.5.0)
WARNING: Added dependency on R >= 3.5.0 because serialized objects in
serialize/load version 3 cannot be read in older versions of R.
File(s) containing such objects:
‘EpiMix.data/data/EPIC_lncRNA_probes.rda’
‘EpiMix.data/data/EPIC_miRNA_probes.rda’
‘EpiMix.data/data/EpigenomeMap.rda’
‘EpiMix.data/data/HM450_lncRNA_probes.rda’
‘EpiMix.data/data/HM450_miRNA_probes.rda’
‘EpiMix.data/data/LUAD.sample.annotation.rda’
‘EpiMix.data/data/MET.data.rda’
‘EpiMix.data/data/Sample_EpiMixResults_Regular.rda’
‘EpiMix.data/data/Sample_EpiMixResults_lncRNA.rda’
‘EpiMix.data/data/Sample_EpiMixResults_miRNA.rda’
‘EpiMix.data/data/TCGA_BatchData.rda’
‘EpiMix.data/data/lncRNA.data.rda’ ‘EpiMix.data/data/mRNA.data.rda’
‘EpiMix.data/data/microRNA.data.rda’
* building ‘EpiMix.data_0.99.0.tar.gz’
nebbiolo1 CHECK output
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===============================
BiocCheckGitClone('EpiMix.data')
===============================
This is BiocCheckGitClone version 1.31.36. 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...
* ERROR: Use Authors@R field not Author/Maintainer fields. Do not
use both.
* 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/2558/EpiMix.data_20220405141730/EpiMix.data.Rcheck’
* using R Under development (unstable) (2022-03-17 r81925)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EpiMix.data/DESCRIPTION’ ... OK
* this is package ‘EpiMix.data’ version ‘0.99.0’
* 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 ‘EpiMix.data’ can be installed ... [13s/13s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
Package in Depends field not imported from: ‘ExperimentHub’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [8s/8s] 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [8s/8s] OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2558/EpiMix.data_20220405141730/EpiMix.data.Rcheck/00check.log’
for details.
===============================
BiocCheck('EpiMix.data_0.99.0.tar.gz')
===============================
This is BiocCheck version 1.31.36. 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/2558/EpiMix.data_20220405141730/EpiMix.data_0.99.0.tar.gz" "/tmp/RtmpyD9XFj/file100dad51d334da/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...
* NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or
removed
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R Version dependency...
* NOTE: Update R version dependency from 3.5.0 to 4.2.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
ExperimentData
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* NOTE: Consider adding these automatically suggested biocViews:
ExpressionData
See http://bioconductor.org/developers/how-to/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...
* ERROR: No 'vignettes' directory.
* Checking whether vignette is built with 'R CMD build'...
* ERROR: Vignette must be built by 'R CMD build'. Please see the
`Vignette Checks` section of the BiocCheck vignette.
* Checking package installation calls in R code...
* Checking for library/require of EpiMix.data...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* Checking man page documentation...
* Checking package NEWS...
* NOTE: Consider adding a NEWS file, so your package news will be
included in Bioconductor release announcements.
* 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; 25 lines (5%) are > 80 characters
long.
First 6 lines:
R/EpiMix.data.R:13 #' A dataframe that maps CpG probes genes to microRN...
R/EpiMix.data.R:25 #' A character vector that maps CpG probes to lncRNA...
R/EpiMix.data.R:37 #' A character vector that maps CpG probes to lncRNA...
R/EpiMix.data.R:50 #' @description The data were generated from the Roa...
R/EpiMix.data.R:54 #' @format A list with 17 elements. The names are ep...
R/EpiMix.data.R:63 #' @description This is a subset of DNA methylation ...
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...
* ERROR: Maintainer must subscribe to the bioc-devel mailing list.
Subscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
* ERROR: Maintainer must register at the support site; visit
https://support.bioconductor.org/accounts/signup/ .
Summary:
ERROR count: 4
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
BiocCheck FAILED.
nebbiolo1 BUILD BIN output
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merida1 Summary
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Package: EpiMix.data |
Version: 0.99.0 |
RVersion: 4.2
|
BiocVersion: 3.15
|
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data EpiMix.data |
BuildTime: 0 minutes 0.64 seconds |
CheckCommand: BiocCheckGitClone('EpiMix.data') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch EpiMix.data_0.99.0.tar.gz && BiocCheck('EpiMix.data_0.99.0.tar.gz', `new-package`=TRUE) |
CheckTime: 2 minutes 5.91 seconds |
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh EpiMix.data_0.99.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
BuildBinTime: 0 minutes 18.25 seconds |
PackageFileSize: 1845.46 KiB |
BuildID:: EpiMix.data_20220405141730 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: EpiMix.data. Starting Build package. Starting Check package. Starting Build package. |
PostProcessing: Finished Git clone. Package type: ExperimentData. Installing dependency status: 0. Checking git clone status: 1. Installing package status: 0. Build Package status: 0. Checking Package status: 1. Build Package status: 0. |
merida1 BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘EpiMix.data/DESCRIPTION’ ... OK
* preparing ‘EpiMix.data’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
NB: this package now depends on R (>= 3.5.0)
WARNING: Added dependency on R >= 3.5.0 because serialized objects in
serialize/load version 3 cannot be read in older versions of R.
File(s) containing such objects:
‘EpiMix.data/data/EPIC_lncRNA_probes.rda’
‘EpiMix.data/data/EPIC_miRNA_probes.rda’
‘EpiMix.data/data/EpigenomeMap.rda’
‘EpiMix.data/data/HM450_lncRNA_probes.rda’
‘EpiMix.data/data/HM450_miRNA_probes.rda’
‘EpiMix.data/data/LUAD.sample.annotation.rda’
‘EpiMix.data/data/MET.data.rda’
‘EpiMix.data/data/Sample_EpiMixResults_Regular.rda’
‘EpiMix.data/data/Sample_EpiMixResults_lncRNA.rda’
‘EpiMix.data/data/Sample_EpiMixResults_miRNA.rda’
‘EpiMix.data/data/TCGA_BatchData.rda’
‘EpiMix.data/data/lncRNA.data.rda’ ‘EpiMix.data/data/mRNA.data.rda’
‘EpiMix.data/data/microRNA.data.rda’
* building ‘EpiMix.data_0.99.0.tar.gz’
merida1 CHECK output
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===============================
BiocCheckGitClone('EpiMix.data')
===============================
This is BiocCheckGitClone version 1.31.36. 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...
* ERROR: Use Authors@R field not Author/Maintainer fields. Do not
use both.
* 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 ‘/Users/pkgbuild/packagebuilder/workers/jobs/2558/EpiMix.data_20220405141730/EpiMix.data.Rcheck’
* using R Under development (unstable) (2022-03-17 r81925)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EpiMix.data/DESCRIPTION’ ... OK
* this is package ‘EpiMix.data’ version ‘0.99.0’
* 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 ‘EpiMix.data’ can be installed ... [16s/17s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
Package in Depends field not imported from: ‘ExperimentHub’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [12s/12s] 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [9s/9s] OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2558/EpiMix.data_20220405141730/EpiMix.data.Rcheck/00check.log’
for details.
===============================
BiocCheck('EpiMix.data_0.99.0.tar.gz')
===============================
This is BiocCheck version 1.31.36. 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/2558/EpiMix.data_20220405141730/EpiMix.data_0.99.0.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//Rtmpgls7ie/file1867c5cd7e52d/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...
* NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or
removed
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R Version dependency...
* NOTE: Update R version dependency from 3.5.0 to 4.2.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
ExperimentData
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* NOTE: Consider adding these automatically suggested biocViews:
ExpressionData
See http://bioconductor.org/developers/how-to/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...
* ERROR: No 'vignettes' directory.
* Checking whether vignette is built with 'R CMD build'...
* ERROR: Vignette must be built by 'R CMD build'. Please see the
`Vignette Checks` section of the BiocCheck vignette.
* Checking package installation calls in R code...
* Checking for library/require of EpiMix.data...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* Checking man page documentation...
* Checking package NEWS...
* NOTE: Consider adding a NEWS file, so your package news will be
included in Bioconductor release announcements.
* 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; 25 lines (5%) are > 80 characters
long.
First 6 lines:
R/EpiMix.data.R:13 #' A dataframe that maps CpG probes genes to microRN...
R/EpiMix.data.R:25 #' A character vector that maps CpG probes to lncRNA...
R/EpiMix.data.R:37 #' A character vector that maps CpG probes to lncRNA...
R/EpiMix.data.R:50 #' @description The data were generated from the Roa...
R/EpiMix.data.R:54 #' @format A list with 17 elements. The names are ep...
R/EpiMix.data.R:63 #' @description This is a subset of DNA methylation ...
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...
* ERROR: Maintainer must subscribe to the bioc-devel mailing list.
Subscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
* ERROR: Maintainer must register at the support site; visit
https://support.bioconductor.org/accounts/signup/ .
Summary:
ERROR count: 4
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
BiocCheck FAILED.
merida1 BUILD BIN output
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===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir EpiMix.data_0.99.0.tar.gz'
>>>>>>>
* installing *source* package ‘EpiMix.data’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (EpiMix.data)