Bioconductor Single Package Builder - Build History

Snapshot Date:

URL: https://git.bioconductor.org/packages/Motif2Site

Last Changed Rev: / Revision:

Last Changed Date:

Hostname	OS /Arch	BUILD	CHECK	BUILD BIN	POST-PROCESSING
merida1	macOS 10.14.6 Mojave/x86_64	OK	OK	OK	OK
nebbiolo1	Linux (Ubuntu 20.04.4 LTS)/x86_64	OK	OK	skipped	OK

merida1 Summary

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Package: Motif2Site

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 Motif2Site

BuildTime: 2 minutes 30.70 seconds

CheckCommand: BiocCheckGitClone('Motif2Site') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Motif2Site_0.99.1.tar.gz && BiocCheck('Motif2Site_0.99.1.tar.gz', `new-package`=TRUE)

CheckTime: 5 minutes 16.47 seconds

BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh Motif2Site_0.99.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir

BuildBinTime: 0 minutes 3.57 seconds

PackageFileSize: 1168.39 KiB

BuildID:: Motif2Site_20220109155601

PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: Motif2Site. 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 ‘Motif2Site/DESCRIPTION’ ... OK
* preparing ‘Motif2Site’:
* 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
Omitted ‘LazyData’ from DESCRIPTION
* building ‘Motif2Site_0.99.1.tar.gz’

merida1 CHECK output

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===============================

 BiocCheckGitClone('Motif2Site')

===============================

This is BiocCheckGitClone version 1.31.22. 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/2429/4f6765b8e88ad5160e2a5b90ca5117a93ec96c7e/Motif2Site.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 ‘Motif2Site/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Motif2Site’ 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:
  .gitignoreommit
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 serialization versions ... OK
* checking whether package ‘Motif2Site’ can be installed ... [3s/3s] 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 ... [5s/5s] 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 ... [273s/274s] OK
Examples with CPU (user + system) or elapsed time > 5s
                                        user system elapsed
pairwisDifferential                   86.044  0.647  86.697
recenterBindingSitesAcrossExperiments 85.655  0.702  86.360
DetectBindingSitesBed                 43.881  0.716  44.602
DetectBindingSitesMotif               34.545  0.186  34.732
compareMotifs2UserProvidedRegions     10.899  0.058  10.958
* 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/2429/4f6765b8e88ad5160e2a5b90ca5117a93ec96c7e/Motif2Site.Rcheck/00check.log’
for details.






===============================

 BiocCheck('Motif2Site_0.99.1.tar.gz')

===============================

This is BiocCheck version 1.31.22. 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...
* 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...
    * NOTE: Consider adding these automatically suggested biocViews:
      Normalization
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...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of Motif2Site...
* Checking coding practice...
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
      Found in files:
        Motif2Site.R (line 86, column 17)
        Motif2Site.R (line 121, column 26)
        Motif2Site.R (line 122, column 25)
        Motif2Site.R (line 123, column 17)
        Motif2Site.R (line 184, column 14)
        Motif2Site.R (line 195, column 17)
        Motif2Site.R (line 205, column 17)
        Motif2Site.R (line 325, column 15)
        Motif2Site.R (line 339, column 15)
        Motif2Site.R (line 378, column 26)
        Motif2Site.R (line 379, column 25)
        Motif2Site.R (line 381, column 17)
        Motif2Site.R (line 470, column 16)
        Motif2Site.R (line 490, column 19)
        Motif2Site.R (line 627, column 40)
        Motif2Site.R (line 630, column 14)
        Motif2Site.R (line 632, column 15)
        Motif2Site.R (line 665, column 13)
        Motif2Site.R (line 678, column 12)
        Motif2Site.R (line 690, column 27)
        Motif2Site.R (line 713, column 18)
        Motif2Site.R (line 875, column 15)
        Motif2Site.R (line 888, column 19)
        Motif2Site.R (line 1034, column 16)
        Motif2Site.R (line 1108, column 15)
        Motif2Site.R (line 1134, column 15)
        Motif2Site.R (line 1159, column 58)
        Motif2Site.R (line 1183, column 17)
        Motif2Site.R (line 1237, column 30)
        Motif2Site.R (line 1246, column 34)
        Motif2Site.R (line 1247, column 35)
        Motif2Site.R (line 1248, column 46)
        Motif2Site.R (line 1249, column 49)
        Motif2Site.R (line 1252, column 14)
        Motif2Site.R (line 1258, column 22)
        Motif2Site.R (line 1270, column 36)
        Motif2Site.R (line 1349, column 55)
        Motif2Site.R (line 1402, column 15)
        Motif2Site.R (line 1524, column 21)
        Motif2Site.R (line 1525, column 24)
        Motif2Site.R (line 1526, column 15)
        Motif2Site.R (line 1714, column 59)
        Motif2Site.R (line 1716, column 43)
        Motif2Site.R (line 1717, column 53)
        Motif2Site.R (line 1718, column 15)
        Motif2Site.R (line 1811, column 34)
        Motif2Site.R (line 1815, column 19)
        Motif2Site.R (line 1816, column 19)
        Motif2Site.R (line 1817, column 26)
        Motif2Site.R (line 1818, column 26)
        Motif2Site.R (line 1821, column 39)
        Motif2Site.R (line 1822, column 15)
        Motif2Site.R (line 1845, column 47)
        Motif2Site.R (line 1849, column 32)
        Motif2Site.R (line 1855, column 14)
        Motif2Site.R (line 1870, column 47)
        Motif2Site.R (line 1905, column 13)
        Motif2Site.R (line 1952, column 28)
        Motif2Site.R (line 1972, column 13)
        Motif2Site.R (line 2040, column 14)
        Motif2Site.R (line 2041, column 15)
        Motif2Site.R (line 2103, column 16)
        Motif2Site.R (line 2268, column 19)
        Motif2Site.R (line 2486, column 14)
        Motif2Site.R (line 2529, column 14)
        Motif2Site.R (line 2550, column 36)
        Motif2Site.R (line 2553, column 52)
        Motif2Site.R (line 2566, column 14)
        Motif2Site.R (line 2672, column 14)
        Motif2Site.R (line 2722, column 14)
        Motif2Site.R (line 2742, column 36)
        Motif2Site.R (line 2745, column 52)
        Motif2Site.R (line 2767, column 14)
        Motif2Site.R (line 2915, column 45)
        Motif2Site.R (line 2947, column 58)
        Motif2Site.R (line 3047, column 14)
        Motif2Site.R (line 3160, column 14)
        Motif2Site.R (line 3198, column 49)
        Motif2Site.R (line 3208, column 33)
        Motif2Site.R (line 3216, column 14)
        Motif2Site.R (line 3256, column 14)
    * NOTE: Avoid the use of 'paste' in condition signals
      Found in files:
        R/Motif2Site.R (line 25, column 10)
        R/Motif2Site.R (line 188, column 13)
        R/Motif2Site.R (line 461, column 10)
        R/Motif2Site.R (line 605, column 13)
        R/Motif2Site.R (line 610, column 13)
        R/Motif2Site.R (line 636, column 13)
        R/Motif2Site.R (line 834, column 13)
        R/Motif2Site.R (line 839, column 13)
        R/Motif2Site.R (line 844, column 13)
        R/Motif2Site.R (line 894, column 13)
        R/Motif2Site.R (line 894, column 42)
        R/Motif2Site.R (line 1221, column 13)
        R/Motif2Site.R (line 1226, column 12)
        R/Motif2Site.R (line 1463, column 10)
        R/Motif2Site.R (line 1502, column 10)
        R/Motif2Site.R (line 1507, column 10)
        R/Motif2Site.R (line 1591, column 10)
        R/Motif2Site.R (line 1596, column 10)
        R/Motif2Site.R (line 1654, column 12)
        R/Motif2Site.R (line 1659, column 12)
        R/Motif2Site.R (line 1696, column 10)
        R/Motif2Site.R (line 1723, column 12)
        R/Motif2Site.R (line 1733, column 12)
        R/Motif2Site.R (line 1744, column 12)
        R/Motif2Site.R (line 1788, column 10)
        R/Motif2Site.R (line 1793, column 11)
        R/Motif2Site.R (line 2014, column 13)
        R/Motif2Site.R (line 2019, column 13)
        R/Motif2Site.R (line 2024, column 13)
        R/Motif2Site.R (line 2474, column 10)
        R/Motif2Site.R (line 2490, column 12)
        R/Motif2Site.R (line 2494, column 12)
        R/Motif2Site.R (line 2513, column 10)
        R/Motif2Site.R (line 2676, column 12)
        R/Motif2Site.R (line 2680, column 12)
        R/Motif2Site.R (line 2705, column 10)
        R/Motif2Site.R (line 3056, column 14)
        R/Motif2Site.R (line 3071, column 12)
        R/Motif2Site.R (line 3088, column 12)
        R/Motif2Site.R (line 3111, column 10)
        R/Motif2Site.R (line 3120, column 14)
        R/Motif2Site.R (line 3127, column 14)
        R/Motif2Site.R (line 3142, column 12)
        R/Motif2Site.R (line 3165, column 12)
        R/Motif2Site.R (line 3171, column 12)
        R/Motif2Site.R (line 3177, column 12)
    * NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
      Found in files:
        R/Motif2Site.R (line 1399, column 10)
        R/Motif2Site.R (line 1512, column 11)
        R/Motif2Site.R (line 1518, column 11)
        R/Motif2Site.R (line 1701, column 11)
        R/Motif2Site.R (line 1723, column 19)
        R/Motif2Site.R (line 1733, column 19)
        R/Motif2Site.R (line 1744, column 19)
        R/Motif2Site.R (line 1949, column 12)
* Checking parsed R code in R directory, examples, vignettes...
    * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3
      times)
        suppressWarnings() in R/Motif2Site.R (line 1412, column 21)
        suppressWarnings() in R/Motif2Site.R (line 1421, column 21)
        suppressWarnings() in R/Motif2Site.R (line 1951, column 21)
* Checking function lengths...
    * NOTE: Recommended function length <= 50 lines.
      There are 18 functions > 50 lines.
      The longest 5 functions are:
        decomposeBindingSignal() (R/Motif2Site.R, line 826): 255 lines
        recenterBindingSitesAcrossExperiments() (R/Motif2Site.R, line
      3023): 243 lines
        motifTablePreProcess() (R/Motif2Site.R, line 1783): 208 lines
        deriveHeuristicBindingDistribution() (R/Motif2Site.R, line
      598): 152 lines
        DetectBindingSitesMotif() (R/Motif2Site.R, line 2659): 140
      lines
* Checking man page documentation...
* Checking package NEWS...
* 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; 20 lines (0%) are > 80 characters
      long.
    First 6 lines:
      R/Motif2Site.R:3182     motifLocations <- Bed2Granges(file.path(as.char...
      vignettes/Motif2Site.Rmd:2 title: "Motif2Site: an R package to detect b...
      vignettes/Motif2Site.Rmd:28 Motif2Stie is an R package to detect transc...
      vignettes/Motif2Site.Rmd:34 Transcription factors often bind to specifi...
      vignettes/Motif2Site.Rmd:36 **Motif2Site** gets two different input, mo...
      vignettes/Motif2Site.Rmd:38 Negative binomial distribution is used to m...
    * NOTE: Consider multiples of 4 spaces for line indents, 1607
      lines(34%) are not.
    First 6 lines:
      R/Motif2Site.R:24   if (!(file.exists(fileName))){
      R/Motif2Site.R:26   }
      R/Motif2Site.R:28   Table <- utils::read.table(fileName, header=FALSE, ...
      R/Motif2Site.R:30   if (length(Table[1,])<3)
      R/Motif2Site.R:31   {
      R/Motif2Site.R:33   }
    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: 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

merida1 BUILD BIN output

[top]

===============================

 R CMD BUILD

===============================

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir Motif2Site_0.99.1.tar.gz'
>>>>>>> 

* installing *source* package ‘Motif2Site’ ...
** 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 (Motif2Site)

nebbiolo1 Summary

[top]

Package: Motif2Site

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 Motif2Site

BuildTime: 2 minutes 14.89 seconds

CheckCommand: BiocCheckGitClone('Motif2Site') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings Motif2Site_0.99.1.tar.gz && BiocCheck('Motif2Site_0.99.1.tar.gz', `new-package`=TRUE)

CheckTime: 4 minutes 29.62 seconds

BuildBinCommand:

BuildBinTime:

PackageFileSize: 1170.73 KiB

BuildID:: Motif2Site_20220109155601

PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: Motif2Site. Starting Build package. Starting Check package.

nebbiolo1 BUILD SRC output

[top]

===============================

 R CMD BUILD

===============================

* checking for file ‘Motif2Site/DESCRIPTION’ ... OK
* preparing ‘Motif2Site’:
* 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
Omitted ‘LazyData’ from DESCRIPTION
* building ‘Motif2Site_0.99.1.tar.gz’

nebbiolo1 CHECK output

[top]

===============================

 BiocCheckGitClone('Motif2Site')

===============================

This is BiocCheckGitClone version 1.31.22. 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/2429/4f6765b8e88ad5160e2a5b90ca5117a93ec96c7e/Motif2Site.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 ‘Motif2Site/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Motif2Site’ 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:
  .gitignoreommit
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 serialization versions ... OK
* checking whether package ‘Motif2Site’ can be installed ... [2s/2s] 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 ... [3s/3s] 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 ... [246s/246s] OK
Examples with CPU (user + system) or elapsed time > 5s
                                        user system elapsed
pairwisDifferential                   77.188  0.727  77.918
recenterBindingSitesAcrossExperiments 76.790  0.760  77.552
DetectBindingSitesBed                 37.851  0.672  38.524
DetectBindingSitesMotif               32.961  0.285  33.245
compareMotifs2UserProvidedRegions      9.650  0.080   9.730
* 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
  ‘/home/pkgbuild/packagebuilder/workers/jobs/2429/4f6765b8e88ad5160e2a5b90ca5117a93ec96c7e/Motif2Site.Rcheck/00check.log’
for details.






===============================

 BiocCheck('Motif2Site_0.99.1.tar.gz')

===============================

This is BiocCheck version 1.31.22. 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...
* 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...
    * NOTE: Consider adding these automatically suggested biocViews:
      Normalization
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...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of Motif2Site...
* Checking coding practice...
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
      Found in files:
        Motif2Site.R (line 86, column 17)
        Motif2Site.R (line 121, column 26)
        Motif2Site.R (line 122, column 25)
        Motif2Site.R (line 123, column 17)
        Motif2Site.R (line 184, column 14)
        Motif2Site.R (line 195, column 17)
        Motif2Site.R (line 205, column 17)
        Motif2Site.R (line 325, column 15)
        Motif2Site.R (line 339, column 15)
        Motif2Site.R (line 378, column 26)
        Motif2Site.R (line 379, column 25)
        Motif2Site.R (line 381, column 17)
        Motif2Site.R (line 470, column 16)
        Motif2Site.R (line 490, column 19)
        Motif2Site.R (line 627, column 40)
        Motif2Site.R (line 630, column 14)
        Motif2Site.R (line 632, column 15)
        Motif2Site.R (line 665, column 13)
        Motif2Site.R (line 678, column 12)
        Motif2Site.R (line 690, column 27)
        Motif2Site.R (line 713, column 18)
        Motif2Site.R (line 875, column 15)
        Motif2Site.R (line 888, column 19)
        Motif2Site.R (line 1034, column 16)
        Motif2Site.R (line 1108, column 15)
        Motif2Site.R (line 1134, column 15)
        Motif2Site.R (line 1159, column 58)
        Motif2Site.R (line 1183, column 17)
        Motif2Site.R (line 1237, column 30)
        Motif2Site.R (line 1246, column 34)
        Motif2Site.R (line 1247, column 35)
        Motif2Site.R (line 1248, column 46)
        Motif2Site.R (line 1249, column 49)
        Motif2Site.R (line 1252, column 14)
        Motif2Site.R (line 1258, column 22)
        Motif2Site.R (line 1270, column 36)
        Motif2Site.R (line 1349, column 55)
        Motif2Site.R (line 1402, column 15)
        Motif2Site.R (line 1524, column 21)
        Motif2Site.R (line 1525, column 24)
        Motif2Site.R (line 1526, column 15)
        Motif2Site.R (line 1714, column 59)
        Motif2Site.R (line 1716, column 43)
        Motif2Site.R (line 1717, column 53)
        Motif2Site.R (line 1718, column 15)
        Motif2Site.R (line 1811, column 34)
        Motif2Site.R (line 1815, column 19)
        Motif2Site.R (line 1816, column 19)
        Motif2Site.R (line 1817, column 26)
        Motif2Site.R (line 1818, column 26)
        Motif2Site.R (line 1821, column 39)
        Motif2Site.R (line 1822, column 15)
        Motif2Site.R (line 1845, column 47)
        Motif2Site.R (line 1849, column 32)
        Motif2Site.R (line 1855, column 14)
        Motif2Site.R (line 1870, column 47)
        Motif2Site.R (line 1905, column 13)
        Motif2Site.R (line 1952, column 28)
        Motif2Site.R (line 1972, column 13)
        Motif2Site.R (line 2040, column 14)
        Motif2Site.R (line 2041, column 15)
        Motif2Site.R (line 2103, column 16)
        Motif2Site.R (line 2268, column 19)
        Motif2Site.R (line 2486, column 14)
        Motif2Site.R (line 2529, column 14)
        Motif2Site.R (line 2550, column 36)
        Motif2Site.R (line 2553, column 52)
        Motif2Site.R (line 2566, column 14)
        Motif2Site.R (line 2672, column 14)
        Motif2Site.R (line 2722, column 14)
        Motif2Site.R (line 2742, column 36)
        Motif2Site.R (line 2745, column 52)
        Motif2Site.R (line 2767, column 14)
        Motif2Site.R (line 2915, column 45)
        Motif2Site.R (line 2947, column 58)
        Motif2Site.R (line 3047, column 14)
        Motif2Site.R (line 3160, column 14)
        Motif2Site.R (line 3198, column 49)
        Motif2Site.R (line 3208, column 33)
        Motif2Site.R (line 3216, column 14)
        Motif2Site.R (line 3256, column 14)
    * NOTE: Avoid the use of 'paste' in condition signals
      Found in files:
        R/Motif2Site.R (line 25, column 10)
        R/Motif2Site.R (line 188, column 13)
        R/Motif2Site.R (line 461, column 10)
        R/Motif2Site.R (line 605, column 13)
        R/Motif2Site.R (line 610, column 13)
        R/Motif2Site.R (line 636, column 13)
        R/Motif2Site.R (line 834, column 13)
        R/Motif2Site.R (line 839, column 13)
        R/Motif2Site.R (line 844, column 13)
        R/Motif2Site.R (line 894, column 13)
        R/Motif2Site.R (line 894, column 42)
        R/Motif2Site.R (line 1221, column 13)
        R/Motif2Site.R (line 1226, column 12)
        R/Motif2Site.R (line 1463, column 10)
        R/Motif2Site.R (line 1502, column 10)
        R/Motif2Site.R (line 1507, column 10)
        R/Motif2Site.R (line 1591, column 10)
        R/Motif2Site.R (line 1596, column 10)
        R/Motif2Site.R (line 1654, column 12)
        R/Motif2Site.R (line 1659, column 12)
        R/Motif2Site.R (line 1696, column 10)
        R/Motif2Site.R (line 1723, column 12)
        R/Motif2Site.R (line 1733, column 12)
        R/Motif2Site.R (line 1744, column 12)
        R/Motif2Site.R (line 1788, column 10)
        R/Motif2Site.R (line 1793, column 11)
        R/Motif2Site.R (line 2014, column 13)
        R/Motif2Site.R (line 2019, column 13)
        R/Motif2Site.R (line 2024, column 13)
        R/Motif2Site.R (line 2474, column 10)
        R/Motif2Site.R (line 2490, column 12)
        R/Motif2Site.R (line 2494, column 12)
        R/Motif2Site.R (line 2513, column 10)
        R/Motif2Site.R (line 2676, column 12)
        R/Motif2Site.R (line 2680, column 12)
        R/Motif2Site.R (line 2705, column 10)
        R/Motif2Site.R (line 3056, column 14)
        R/Motif2Site.R (line 3071, column 12)
        R/Motif2Site.R (line 3088, column 12)
        R/Motif2Site.R (line 3111, column 10)
        R/Motif2Site.R (line 3120, column 14)
        R/Motif2Site.R (line 3127, column 14)
        R/Motif2Site.R (line 3142, column 12)
        R/Motif2Site.R (line 3165, column 12)
        R/Motif2Site.R (line 3171, column 12)
        R/Motif2Site.R (line 3177, column 12)
    * NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
      Found in files:
        R/Motif2Site.R (line 1399, column 10)
        R/Motif2Site.R (line 1512, column 11)
        R/Motif2Site.R (line 1518, column 11)
        R/Motif2Site.R (line 1701, column 11)
        R/Motif2Site.R (line 1723, column 19)
        R/Motif2Site.R (line 1733, column 19)
        R/Motif2Site.R (line 1744, column 19)
        R/Motif2Site.R (line 1949, column 12)
* Checking parsed R code in R directory, examples, vignettes...
    * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3
      times)
        suppressWarnings() in R/Motif2Site.R (line 1412, column 21)
        suppressWarnings() in R/Motif2Site.R (line 1421, column 21)
        suppressWarnings() in R/Motif2Site.R (line 1951, column 21)
* Checking function lengths...
    * NOTE: Recommended function length <= 50 lines.
      There are 18 functions > 50 lines.
      The longest 5 functions are:
        decomposeBindingSignal() (R/Motif2Site.R, line 826): 255 lines
        recenterBindingSitesAcrossExperiments() (R/Motif2Site.R, line
      3023): 243 lines
        motifTablePreProcess() (R/Motif2Site.R, line 1783): 208 lines
        deriveHeuristicBindingDistribution() (R/Motif2Site.R, line
      598): 152 lines
        DetectBindingSitesMotif() (R/Motif2Site.R, line 2659): 140
      lines
* Checking man page documentation...
* Checking package NEWS...
* 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; 20 lines (0%) are > 80 characters
      long.
    First 6 lines:
      R/Motif2Site.R:3182     motifLocations <- Bed2Granges(file.path(as.char...
      vignettes/Motif2Site.Rmd:2 title: "Motif2Site: an R package to detect b...
      vignettes/Motif2Site.Rmd:28 Motif2Stie is an R package to detect transc...
      vignettes/Motif2Site.Rmd:34 Transcription factors often bind to specifi...
      vignettes/Motif2Site.Rmd:36 **Motif2Site** gets two different input, mo...
      vignettes/Motif2Site.Rmd:38 Negative binomial distribution is used to m...
    * NOTE: Consider multiples of 4 spaces for line indents, 1607
      lines(34%) are not.
    First 6 lines:
      R/Motif2Site.R:24   if (!(file.exists(fileName))){
      R/Motif2Site.R:26   }
      R/Motif2Site.R:28   Table <- utils::read.table(fileName, header=FALSE, ...
      R/Motif2Site.R:30   if (length(Table[1,])<3)
      R/Motif2Site.R:31   {
      R/Motif2Site.R:33   }
    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: 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

nebbiolo1 BUILD BIN output

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