===============================
BiocCheckGitClone('RolDE')
===============================
This is BiocCheckGitClone version 1.31.34. 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/2442/1f75235c8425338ed16b9c184205ee5cccbf6499/RolDE.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 ‘RolDE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RolDE’ version ‘0.99.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘RolDE’ can be installed ... [34s/34s] 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 ... [44s/51s] OK
* checking Rd files ... [1s/1s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'RolDE.Rd':
\examples lines wider than 100 characters:
#Default usage of RolDE in a small example time point aligned data without significance value estimation and 1 core
Rd file 'RolDE_Main.Rd':
\examples lines wider than 100 characters:
#Default usage of RolDE in a small example time point aligned data without significance value estimation and 1 core
These lines will be truncated in the PDF manual.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [13s/184s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
RolDE 0.712 0.068 82.905
RolDE_Main 0.657 0.023 88.801
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2442/1f75235c8425338ed16b9c184205ee5cccbf6499/RolDE.Rcheck/00check.log’
for details.
===============================
BiocCheck('RolDE_0.99.1.tar.gz')
===============================
This is BiocCheck version 1.31.34. 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/2442/1f75235c8425338ed16b9c184205ee5cccbf6499/RolDE_0.99.1.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpAkul6k/file211a6386fad/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 3.1.0 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 RolDE...
* Checking coding practice...
* NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
determineDegrees.R (line 16, column 14)
determineROTSRuns.R (line 11, column 16)
determineROTSRuns.R (line 14, column 18)
determineROTSRuns.R (line 45, column 14)
determineROTSRuns.R (line 64, column 13)
determineROTSRuns.R (line 67, column 12)
determineROTSRuns.R (line 71, column 14)
DiffROTSAligned.R (line 43, column 42)
DiffROTSAligned.R (line 48, column 35)
DiffROTSAligned.R (line 58, column 17)
DiffROTSAligned.R (line 71, column 14)
DiffROTSAligned.R (line 75, column 19)
DiffROTSAligned.R (line 96, column 14)
DiffROTSAligned.R (line 97, column 20)
DiffROTSAligned.R (line 124, column 14)
DiffROTSAligned.R (line 133, column 14)
DiffROTSMixNonAligned.R (line 19, column 14)
DiffROTSMixNonAligned.R (line 103, column 33)
DiffROTSNonAligned.R (line 19, column 14)
DiffROTSNonAligned.R (line 81, column 33)
estSigValAlignedWeights.R (line 46, column 34)
estSigValAlignedWeights.R (line 57, column 12)
estSigValNonAlignedWeights.R (line 46, column 34)
estSigValNonAlignedWeights.R (line 57, column 12)
plotFindings.R (line 60, column 12)
plotFindings.R (line 68, column 14)
plotFindings.R (line 98, column 14)
PolyReg.R (line 19, column 35)
PolyReg.R (line 51, column 19)
PolyReg.R (line 67, column 12)
PolyReg.R (line 68, column 63)
PolyReg.R (line 70, column 26)
PolyRegMix.R (line 17, column 35)
PolyRegMix.R (line 51, column 21)
PolyRegMix.R (line 79, column 21)
PolyRegMix.R (line 96, column 12)
PolyRegMix.R (line 97, column 63)
PolyRegMix.R (line 99, column 26)
RegROTS.R (line 21, column 75)
RegROTS.R (line 107, column 15)
RegROTS.R (line 107, column 56)
RegROTS.R (line 107, column 96)
RegROTS.R (line 119, column 42)
RegROTS.R (line 123, column 35)
RegROTS.R (line 133, column 17)
RegROTS.R (line 146, column 14)
RegROTS.R (line 150, column 19)
RegROTS.R (line 175, column 18)
RegROTS.R (line 186, column 18)
RegROTS.R (line 213, column 14)
RegROTS.R (line 222, column 14)
utilFunctions.R (line 18, column 12)
utilFunctions.R (line 27, column 12)
utilFunctions.R (line 34, column 12)
utilFunctions.R (line 43, column 12)
utilFunctions.R (line 48, column 12)
utilFunctions.R (line 58, column 14)
utilFunctions.R (line 68, column 14)
utilFunctions.R (line 69, column 16)
utilFunctions.R (line 72, column 19)
utilFunctions.R (line 130, column 12)
utilFunctions.R (line 140, column 16)
utilFunctions.R (line 145, column 20)
utilFunctions.R (line 147, column 51)
utilFunctions.R (line 156, column 16)
validateInput.R (line 83, column 14)
validateInput.R (line 95, column 15)
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
cat() in R/RolDE_Main.R (line 222, column 37)
cat() in R/RolDE_Main.R (line 245, column 31)
cat() in R/RolDE_Main.R (line 261, column 36)
cat() in R/RolDE_Main.R (line 281, column 33)
cat() in R/RolDE_Main.R (line 302, column 36)
cat() in R/RolDE_Main.R (line 335, column 36)
cat() in R/RolDE_Main.R (line 376, column 33)
cat() in R/RolDE_Main.R (line 394, column 35)
cat() in R/RolDE_Main.R (line 423, column 31)
cat() in R/RolDE.R (line 177, column 29)
* NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
R/calculateRP.R (line 13, column 13)
R/calculateRP.R (line 16, column 80)
R/determineDegrees.R (line 23, column 40)
R/determineDegrees.R (line 28, column 40)
R/determineDegrees.R (line 35, column 14)
R/determineDegrees.R (line 36, column 21)
R/determineROTSRuns.R (line 8, column 8)
R/determineROTSRuns.R (line 9, column 18)
R/determineROTSRuns.R (line 12, column 15)
R/determineROTSRuns.R (line 13, column 15)
R/determineROTSRuns.R (line 15, column 17)
R/determineROTSRuns.R (line 16, column 17)
R/determineROTSRuns.R (line 17, column 23)
R/determineROTSRuns.R (line 19, column 14)
R/determineROTSRuns.R (line 51, column 38)
R/determineROTSRuns.R (line 55, column 11)
R/DiffROTSAligned.R (line 18, column 10)
R/DiffROTSAligned.R (line 19, column 17)
R/DiffROTSAligned.R (line 20, column 14)
R/DiffROTSAligned.R (line 21, column 14)
R/DiffROTSAligned.R (line 26, column 16)
R/DiffROTSAligned.R (line 30, column 39)
R/DiffROTSAligned.R (line 31, column 24)
R/DiffROTSAligned.R (line 32, column 14)
R/DiffROTSAligned.R (line 40, column 17)
R/DiffROTSAligned.R (line 62, column 28)
R/DiffROTSAligned.R (line 63, column 25)
R/DiffROTSAligned.R (line 87, column 78)
R/DiffROTSAligned.R (line 98, column 13)
R/DiffROTSAligned.R (line 99, column 62)
R/DiffROTSAligned.R (line 100, column 33)
R/DiffROTSAligned.R (line 104, column 13)
R/DiffROTSAligned.R (line 108, column 16)
R/DiffROTSAligned.R (line 109, column 17)
R/DiffROTSAligned.R (line 166, column 69)
R/DiffROTSAligned.R (line 167, column 81)
R/DiffROTSAligned.R (line 169, column 14)
R/DiffROTSAligned.R (line 170, column 14)
R/DiffROTSMixNonAligned.R (line 9, column 13)
R/DiffROTSMixNonAligned.R (line 73, column 14)
R/DiffROTSMixNonAligned.R (line 74, column 66)
R/DiffROTSMixNonAligned.R (line 82, column 9)
R/DiffROTSMixNonAligned.R (line 83, column 9)
R/DiffROTSMixNonAligned.R (line 84, column 10)
R/DiffROTSMixNonAligned.R (line 85, column 10)
R/DiffROTSMixNonAligned.R (line 86, column 9)
R/DiffROTSMixNonAligned.R (line 87, column 9)
R/DiffROTSMixNonAligned.R (line 89, column 18)
R/DiffROTSMixNonAligned.R (line 102, column 23)
R/DiffROTSMixNonAligned.R (line 103, column 23)
R/DiffROTSMixNonAligned.R (line 118, column 11)
R/DiffROTSNonAligned.R (line 9, column 13)
R/DiffROTSNonAligned.R (line 51, column 14)
R/DiffROTSNonAligned.R (line 52, column 66)
R/DiffROTSNonAligned.R (line 60, column 9)
R/DiffROTSNonAligned.R (line 61, column 9)
R/DiffROTSNonAligned.R (line 62, column 10)
R/DiffROTSNonAligned.R (line 63, column 10)
R/DiffROTSNonAligned.R (line 64, column 9)
R/DiffROTSNonAligned.R (line 65, column 9)
R/DiffROTSNonAligned.R (line 67, column 18)
R/DiffROTSNonAligned.R (line 71, column 13)
R/DiffROTSNonAligned.R (line 80, column 23)
R/DiffROTSNonAligned.R (line 81, column 23)
R/DiffROTSNonAligned.R (line 96, column 11)
R/estSigValAlignedWeights.R (line 12, column 18)
R/estSigValAlignedWeights.R (line 16, column 19)
R/estSigValAlignedWeights.R (line 20, column 17)
R/estSigValAlignedWeights.R (line 37, column 17)
R/estSigValAlignedWeights.R (line 38, column 11)
R/estSigValAlignedWeights.R (line 54, column 13)
R/estSigValAlignedWeights.R (line 56, column 13)
R/estSigValAlignedWeights.R (line 59, column 20)
R/estSigValAlignedWeights.R (line 61, column 20)
R/estSigValAlignedWeights.R (line 74, column 20)
R/estSigValAlignedWeights.R (line 76, column 14)
R/estSigValAlignedWeights.R (line 77, column 14)
R/estSigValAlignedWeights.R (line 78, column 14)
R/estSigValAlignedWeights.R (line 79, column 14)
R/estSigValNonAlignedWeights.R (line 12, column 18)
R/estSigValNonAlignedWeights.R (line 16, column 19)
R/estSigValNonAlignedWeights.R (line 20, column 17)
R/estSigValNonAlignedWeights.R (line 37, column 17)
R/estSigValNonAlignedWeights.R (line 38, column 11)
R/estSigValNonAlignedWeights.R (line 54, column 13)
R/estSigValNonAlignedWeights.R (line 56, column 13)
R/estSigValNonAlignedWeights.R (line 59, column 20)
R/estSigValNonAlignedWeights.R (line 61, column 20)
R/estSigValNonAlignedWeights.R (line 74, column 20)
R/estSigValNonAlignedWeights.R (line 76, column 14)
R/estSigValNonAlignedWeights.R (line 77, column 14)
R/estSigValNonAlignedWeights.R (line 78, column 14)
R/estSigValNonAlignedWeights.R (line 79, column 14)
R/plotFindings.R (line 27, column 10)
R/plotFindings.R (line 28, column 10)
R/plotFindings.R (line 29, column 9)
R/plotFindings.R (line 30, column 12)
R/plotFindings.R (line 31, column 11)
R/plotFindings.R (line 33, column 11)
R/plotFindings.R (line 34, column 21)
R/plotFindings.R (line 42, column 13)
R/plotFindings.R (line 43, column 13)
R/plotFindings.R (line 44, column 13)
R/plotFindings.R (line 46, column 17)
R/plotFindings.R (line 47, column 17)
R/plotFindings.R (line 49, column 19)
R/plotFindings.R (line 51, column 13)
R/plotFindings.R (line 52, column 13)
R/plotFindings.R (line 61, column 16)
R/plotFindings.R (line 62, column 16)
R/plotFindings.R (line 63, column 14)
R/plotFindings.R (line 64, column 12)
R/plotFindings.R (line 67, column 20)
R/plotFindings.R (line 69, column 16)
R/plotFindings.R (line 70, column 15)
R/plotFindings.R (line 72, column 15)
R/plotFindings.R (line 74, column 8)
R/plotFindings.R (line 75, column 11)
R/plotFindings.R (line 76, column 15)
R/plotFindings.R (line 78, column 30)
R/plotFindings.R (line 79, column 34)
R/plotFindings.R (line 80, column 27)
R/plotFindings.R (line 82, column 8)
R/plotFindings.R (line 97, column 20)
R/plotFindings.R (line 99, column 16)
R/plotFindings.R (line 100, column 15)
R/plotFindings.R (line 102, column 15)
R/plotFindings.R (line 104, column 8)
R/plotFindings.R (line 105, column 11)
R/plotFindings.R (line 106, column 15)
R/plotFindings.R (line 108, column 30)
R/plotFindings.R (line 109, column 34)
R/plotFindings.R (line 110, column 27)
R/plotFindings.R (line 112, column 8)
R/PolyReg.R (line 62, column 80)
R/PolyReg.R (line 63, column 92)
R/PolyReg.R (line 66, column 17)
R/PolyReg.R (line 68, column 27)
R/PolyReg.R (line 70, column 12)
R/PolyReg.R (line 79, column 11)
R/PolyRegMix.R (line 30, column 12)
R/PolyRegMix.R (line 58, column 12)
R/PolyRegMix.R (line 91, column 80)
R/PolyRegMix.R (line 92, column 92)
R/PolyRegMix.R (line 95, column 17)
R/PolyRegMix.R (line 97, column 27)
R/PolyRegMix.R (line 99, column 12)
R/PolyRegMix.R (line 108, column 11)
R/RegROTS.R (line 114, column 17)
R/RegROTS.R (line 137, column 28)
R/RegROTS.R (line 138, column 25)
R/RegROTS.R (line 164, column 78)
R/RegROTS.R (line 258, column 69)
R/RegROTS.R (line 259, column 81)
R/RolDE_Main.R (line 337, column 21)
R/utilFunctions.R (line 47, column 12)
R/utilFunctions.R (line 49, column 14)
R/utilFunctions.R (line 50, column 19)
R/utilFunctions.R (line 60, column 15)
R/utilFunctions.R (line 61, column 19)
R/utilFunctions.R (line 74, column 21)
R/utilFunctions.R (line 82, column 13)
R/utilFunctions.R (line 83, column 15)
R/utilFunctions.R (line 91, column 25)
R/utilFunctions.R (line 100, column 27)
R/utilFunctions.R (line 124, column 36)
R/utilFunctions.R (line 125, column 15)
R/utilFunctions.R (line 158, column 15)
R/utilFunctions.R (line 174, column 9)
R/utilFunctions.R (line 193, column 18)
R/utilFunctions.R (line 198, column 9)
R/utilFunctions.R (line 199, column 56)
R/utilFunctions.R (line 213, column 11)
R/utilFunctions.R (line 214, column 72)
R/utilFunctions.R (line 226, column 63)
R/utilFunctions.R (line 246, column 20)
R/utilFunctions.R (line 252, column 20)
R/utilFunctions.R (line 258, column 20)
R/utilFunctions.R (line 261, column 12)
R/utilFunctions.R (line 281, column 20)
R/utilFunctions.R (line 287, column 20)
R/utilFunctions.R (line 293, column 20)
R/utilFunctions.R (line 296, column 12)
R/validateInput.R (line 37, column 14)
R/validateInput.R (line 40, column 14)
R/validateInput.R (line 63, column 20)
R/validateInput.R (line 105, column 13)
R/validateInput.R (line 106, column 23)
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
R/calculateRP.R (line 23, column 36)
R/determineDegrees.R (line 32, column 13)
R/DiffROTSAligned.R (line 172, column 36)
R/DiffROTSMixNonAligned.R (line 117, column 36)
R/DiffROTSNonAligned.R (line 95, column 36)
R/estSigValAlignedWeights.R (line 81, column 36)
R/estSigValNonAlignedWeights.R (line 81, column 36)
R/PolyReg.R (line 77, column 38)
R/PolyRegMix.R (line 106, column 38)
R/RegROTS.R (line 264, column 36)
R/RolDE_Main.R (line 215, column 15)
R/RolDE_Main.R (line 222, column 41)
R/RolDE_Main.R (line 238, column 15)
R/RolDE_Main.R (line 245, column 35)
R/RolDE_Main.R (line 254, column 15)
R/RolDE_Main.R (line 261, column 40)
R/RolDE_Main.R (line 274, column 15)
R/RolDE_Main.R (line 281, column 37)
R/RolDE_Main.R (line 296, column 17)
R/RolDE_Main.R (line 302, column 40)
R/RolDE_Main.R (line 316, column 19)
R/RolDE_Main.R (line 327, column 19)
R/RolDE_Main.R (line 335, column 40)
R/RolDE_Main.R (line 356, column 17)
R/RolDE_Main.R (line 368, column 17)
R/RolDE_Main.R (line 376, column 37)
R/RolDE_Main.R (line 388, column 15)
R/RolDE_Main.R (line 394, column 39)
R/RolDE_Main.R (line 405, column 19)
R/RolDE_Main.R (line 416, column 19)
R/RolDE_Main.R (line 423, column 35)
R/RolDE.R (line 172, column 15)
R/RolDE.R (line 177, column 33)
R/utilFunctions.R (line 126, column 52)
R/validateInput.R (line 34, column 36)
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 6
times)
suppressMessages() in R/DiffROTSAligned.R (line 144, column 5)
suppressWarnings() in R/DiffROTSMixNonAligned.R (line 108,
column 10)
suppressMessages() in R/DiffROTSMixNonAligned.R (line 92,
column 5)
suppressWarnings() in R/DiffROTSNonAligned.R (line 86, column
10)
suppressMessages() in R/DiffROTSNonAligned.R (line 70, column
5)
suppressMessages() in R/RegROTS.R (line 233, column 5)
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 14 functions > 50 lines.
The longest 5 functions are:
RegROTS() (R/RegROTS.R, line 1): 270 lines
RolDE_Main() (R/RolDE_Main.R, line 190): 242 lines
DiffROTSAligned() (R/DiffROTSAligned.R, line 1): 179 lines
validateInput() (R/validateInput.R, line 2): 122 lines
DiffROTSMixNonAligned() (R/DiffROTSMixNonAligned.R, line 1):
121 lines
* 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; 679 lines (20%) are > 80 characters
long.
First 6 lines:
R/calculateRP.R:3 res_diffrots<-res_diffrots[rownames(res_regrots),] ...
R/calculateRP.R:16 if(any(rank_prods=="NaN", na.rm = TRUE)){rank_prod...
R/calculateRP.R:23 if(all(is.na(fin_res[,2]))){stop("Unkown error dur...
R/data1.R:1 #' A proteomics dataset with random protein expression valu...
R/data1.R:4 #' three replicates for each sample at each timepoint in ea...
R/data1.R:5 #' values for the random data have been generated using the...
* NOTE: Consider multiples of 4 spaces for line indents, 973
lines(29%) are not.
First 6 lines:
R/calculateRP.R:3 res_diffrots<-res_diffrots[rownames(res_regrots),] ...
R/calculateRP.R:4 res_polyreg<-res_polyreg[rownames(res_regrots),]
R/calculateRP.R:6 r1<-rank(as.numeric(res_regrots[,2]),ties.method = ...
R/calculateRP.R:7 r2<-rank(as.numeric(res_diffrots[,2]),ties.method =...
R/calculateRP.R:8 r3<-rank(as.numeric(res_polyreg[,2]),ties.method = ...
R/calculateRP.R:10 ranks<-cbind(r1, r2, r3)
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: 12
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