nebbiolo1 Summary
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| Package: Macarron |
| Version: 0.99.1 |
| RVersion: 4.2
|
| BiocVersion: 3.15
|
| BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data Macarron |
| BuildTime: 0 minutes 27.02 seconds |
| CheckCommand: BiocCheckGitClone('Macarron') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings Macarron_0.99.1.tar.gz && BiocCheck('Macarron_0.99.1.tar.gz', `new-package`=TRUE) |
| CheckTime: 3 minutes 13.87 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 609.37 KiB |
| BuildID:: Macarron_20220329183103 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: Macarron. 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: 1. |
nebbiolo1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘Macarron/DESCRIPTION’ ... OK
* preparing ‘Macarron’:
* 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 ‘Macarron_0.99.1.tar.gz’
nebbiolo1 CHECK output
[top]
===============================
BiocCheckGitClone('Macarron')
===============================
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...
* 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/2546/d6a743a388a8b3d17638016829b17bee9ed76eb9/Macarron.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 ‘Macarron/DESCRIPTION’ ... OK
* this is package ‘Macarron’ 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 ... NOTE
Found the following hidden files and directories:
.github
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 ‘Macarron’ can be installed ... [12s/12s] 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] NOTE
calQval: no visible binding for global variable ‘metadata’
calQval: no visible binding for global variable ‘value’
calQval: no visible binding for global variable ‘pval’
Undefined global functions or variables:
metadata pval value
* 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 ... [46s/54s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
MACARRoN 8.714 0.328 9.045
prioritize 5.810 0.104 5.914
showBest 5.655 0.084 5.740
decorateID 0.397 0.020 8.026
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [40s/45s]
[40s/45s] 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/2546/d6a743a388a8b3d17638016829b17bee9ed76eb9/Macarron.Rcheck/00check.log’
for details.
===============================
BiocCheck('Macarron_0.99.1.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/2546/d6a743a388a8b3d17638016829b17bee9ed76eb9/Macarron_0.99.1.tar.gz" "/tmp/RtmpVaBvlq/file249b277cd09742/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...
* 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...
* WARNING: Evaluate more vignette chunks.
# of code chunks: 9
# of eval=FALSE: 7
# of nonexecutable code chunks by syntax: 0
# total unevaluated 7 (77%)
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of Macarron...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
Found in files:
R/calAVA.R (line 135, column 34)
R/calAVA.R (line 137, column 30)
R/calES.R (line 51, column 10)
R/findMacMod.R (line 136, column 20)
R/findMacMod.R (line 153, column 29)
R/findMacMod.R (line 201, column 35)
R/findMacMod.R (line 203, column 36)
R/prioritize.R (line 89, column 40)
* NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
makeDisMat.R (line 122, column 16)
showBest.R (line 102, column 25)
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
print() in R/MACARRoN.R (line 118, column 7)
* NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
R/calQval.R (line 68, column 19)
R/calQval.R (line 70, column 19)
R/findMacMod.R (line 48, column 21)
R/findMacMod.R (line 50, column 21)
R/MACARRoN.R (line 199, column 11)
R/MACARRoN.R (line 201, column 11)
R/MACARRoN.R (line 275, column 14)
R/MACARRoN.R (line 281, column 14)
R/MACARRoN.R (line 299, column 16)
R/makeDisMat.R (line 130, column 8)
R/makeDisMat.R (line 133, column 5)
* NOTE: Avoid the use of 'paste' in condition signals
Found in files:
R/calES.R (line 50, column 13)
R/calES.R (line 61, column 13)
R/makeDisMat.R (line 66, column 11)
R/makeDisMat.R (line 72, column 15)
R/makeDisMat.R (line 101, column 17)
R/makeDisMat.R (line 135, column 11)
R/prepInput.R (line 48, column 11)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 7 functions > 50 lines.
The longest 5 functions are:
Macarron() (R/MACARRoN.R, line 41): 264 lines
findMacMod() (R/findMacMod.R, line 35): 174 lines
makeDisMat() (R/makeDisMat.R, line 30): 107 lines
calAVA() (R/calAVA.R, line 35): 106 lines
prioritize() (R/prioritize.R, line 47): 94 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; 350 lines (16%) are > 80 characters
long.
First 6 lines:
R/calAVA.R:3 #' AVA of a feature is the ratio of its abundance and the ...
R/calAVA.R:4 #' i.e. the "anchor". Anchor is an annotated/known feature...
R/calAVA.R:5 #' feature. For every feature, mean abundance in each phen...
R/calAVA.R:10 #' @param metadata_variable name or index of metadata col...
R/calAVA.R:11 #' Note: metadata_variable must be consistent across dist...
R/calAVA.R:12 #' @param anchor_annotation name or index of column conta...
* NOTE: Consider 4 spaces instead of tabs; 4 lines (0%) contain
tabs.
First 4 lines:
R/calQval.R:19 #' @param plot_heatmap Maaslin2 option-Generate a heatm...
R/calQval.R:20 #' @param plot_scatter Maaslin2 option-Generate scatter...
R/MACARRoN.R:18 #' @param plot_heatmap MaAslin2 option-Generate a heat...
R/MACARRoN.R:19 #' @param plot_scatter MaAslin2 option-Generate scatte...
* NOTE: Consider multiples of 4 spaces for line indents, 592
lines(27%) are not.
First 6 lines:
R/calAVA.R:37 mod.assn,
R/calAVA.R:38 metadata_variable = 1,
R/calAVA.R:39 anchor_annotation = 2)
R/calAVA.R:40 {
R/calAVA.R:41 mod.assn <- as.data.frame(mod.assn[[1]])
R/calAVA.R:42 fint <- as.data.frame(SummarizedExperiment::assay(se))
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...
Maintainer is registered at support site.
Package name is in support site watched tags.
Summary:
ERROR count: 1
WARNING count: 1
NOTE count: 9
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
[top]
| Package: Macarron |
| Version: 0.99.1 |
| RVersion: 4.2
|
| BiocVersion: 3.15
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data Macarron |
| BuildTime: 0 minutes 39.12 seconds |
| CheckCommand: BiocCheckGitClone('Macarron') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Macarron_0.99.1.tar.gz && BiocCheck('Macarron_0.99.1.tar.gz', `new-package`=TRUE) |
| CheckTime: 4 minutes 44.75 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh Macarron_0.99.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 18.04 seconds |
| PackageFileSize: 606.55 KiB |
| BuildID:: Macarron_20220329183103 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: Macarron. 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: 1. Build Package status: 0. |
merida1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘Macarron/DESCRIPTION’ ... OK
* preparing ‘Macarron’:
* 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 ‘Macarron_0.99.1.tar.gz’
merida1 CHECK output
[top]
===============================
BiocCheckGitClone('Macarron')
===============================
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...
* 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/2546/d6a743a388a8b3d17638016829b17bee9ed76eb9/Macarron.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 ‘Macarron/DESCRIPTION’ ... OK
* this is package ‘Macarron’ 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 ... NOTE
Found the following hidden files and directories:
.github
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 ‘Macarron’ can be installed ... [18s/18s] 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] NOTE
calQval: no visible binding for global variable ‘metadata’
calQval: no visible binding for global variable ‘value’
calQval: no visible binding for global variable ‘pval’
Undefined global functions or variables:
metadata pval value
* 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 ... [64s/77s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
MACARRoN 12.680 0.412 13.102
prioritize 8.731 0.151 8.891
showBest 8.689 0.134 8.826
calES 7.090 0.183 7.276
calQval 6.990 0.157 7.150
decorateID 0.214 0.021 13.306
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [55s/62s]
[55s/62s] 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/2546/d6a743a388a8b3d17638016829b17bee9ed76eb9/Macarron.Rcheck/00check.log’
for details.
===============================
BiocCheck('Macarron_0.99.1.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/2546/d6a743a388a8b3d17638016829b17bee9ed76eb9/Macarron_0.99.1.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//Rtmped6oDR/file12935759f551b/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...
* 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...
* WARNING: Evaluate more vignette chunks.
# of code chunks: 9
# of eval=FALSE: 7
# of nonexecutable code chunks by syntax: 0
# total unevaluated 7 (77%)
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of Macarron...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
Found in files:
R/calAVA.R (line 135, column 34)
R/calAVA.R (line 137, column 30)
R/calES.R (line 51, column 10)
R/findMacMod.R (line 136, column 20)
R/findMacMod.R (line 153, column 29)
R/findMacMod.R (line 201, column 35)
R/findMacMod.R (line 203, column 36)
R/prioritize.R (line 89, column 40)
* NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
makeDisMat.R (line 122, column 16)
showBest.R (line 102, column 25)
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
print() in R/MACARRoN.R (line 118, column 7)
* NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
R/calQval.R (line 68, column 19)
R/calQval.R (line 70, column 19)
R/findMacMod.R (line 48, column 21)
R/findMacMod.R (line 50, column 21)
R/MACARRoN.R (line 199, column 11)
R/MACARRoN.R (line 201, column 11)
R/MACARRoN.R (line 275, column 14)
R/MACARRoN.R (line 281, column 14)
R/MACARRoN.R (line 299, column 16)
R/makeDisMat.R (line 130, column 8)
R/makeDisMat.R (line 133, column 5)
* NOTE: Avoid the use of 'paste' in condition signals
Found in files:
R/calES.R (line 50, column 13)
R/calES.R (line 61, column 13)
R/makeDisMat.R (line 66, column 11)
R/makeDisMat.R (line 72, column 15)
R/makeDisMat.R (line 101, column 17)
R/makeDisMat.R (line 135, column 11)
R/prepInput.R (line 48, column 11)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 7 functions > 50 lines.
The longest 5 functions are:
Macarron() (R/MACARRoN.R, line 41): 264 lines
findMacMod() (R/findMacMod.R, line 35): 174 lines
makeDisMat() (R/makeDisMat.R, line 30): 107 lines
calAVA() (R/calAVA.R, line 35): 106 lines
prioritize() (R/prioritize.R, line 47): 94 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; 350 lines (16%) are > 80 characters
long.
First 6 lines:
R/calAVA.R:3 #' AVA of a feature is the ratio of its abundance and the ...
R/calAVA.R:4 #' i.e. the "anchor". Anchor is an annotated/known feature...
R/calAVA.R:5 #' feature. For every feature, mean abundance in each phen...
R/calAVA.R:10 #' @param metadata_variable name or index of metadata col...
R/calAVA.R:11 #' Note: metadata_variable must be consistent across dist...
R/calAVA.R:12 #' @param anchor_annotation name or index of column conta...
* NOTE: Consider 4 spaces instead of tabs; 4 lines (0%) contain
tabs.
First 4 lines:
R/calQval.R:19 #' @param plot_heatmap Maaslin2 option-Generate a heatm...
R/calQval.R:20 #' @param plot_scatter Maaslin2 option-Generate scatter...
R/MACARRoN.R:18 #' @param plot_heatmap MaAslin2 option-Generate a heat...
R/MACARRoN.R:19 #' @param plot_scatter MaAslin2 option-Generate scatte...
* NOTE: Consider multiples of 4 spaces for line indents, 592
lines(27%) are not.
First 6 lines:
R/calAVA.R:37 mod.assn,
R/calAVA.R:38 metadata_variable = 1,
R/calAVA.R:39 anchor_annotation = 2)
R/calAVA.R:40 {
R/calAVA.R:41 mod.assn <- as.data.frame(mod.assn[[1]])
R/calAVA.R:42 fint <- as.data.frame(SummarizedExperiment::assay(se))
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...
Maintainer is registered at support site.
Package name is in support site watched tags.
Summary:
ERROR count: 1
WARNING count: 1
NOTE count: 9
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
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir Macarron_0.99.1.tar.gz'
>>>>>>>
* installing *source* package ‘Macarron’ ...
** using staged installation
** R
** 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 (Macarron)