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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:chopsticks.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings chopsticks_1.58.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/chopsticks.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘chopsticks/DESCRIPTION’ ... OK
* this is package ‘chopsticks’ version ‘1.58.0’
* 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:
  .git_fetch_output.txt
  .git_merge_output.txt
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 ‘chopsticks’ can be installed ... WARNING
Found the following significant warnings:
  glm_test.c:155:14: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Users/biocbuild/bbs-3.13-bioc/meat/chopsticks.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... 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 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 ... OK
* checking Rd files ... NOTE
prepare_Rd: ibs.stats.Rd:28: Dropping empty section \references
prepare_Rd: ibs.stats.Rd:49: Dropping empty section \seealso
prepare_Rd: read.pedfile.info.Rd:31-32: Dropping empty section \examples
prepare_Rd: read.pedfile.map.Rd:31-32: Dropping empty section \examples
prepare_Rd: read.snps.chiamo.Rd:37-38: Dropping empty section \note
prepare_Rd: read.wtccc.signals.Rd:58: Dropping empty section \seealso
prepare_Rd: wtccc.sample.list.Rd:36-37: Dropping empty section \note
prepare_Rd: wtccc.sample.list.Rd:39-40: Dropping empty section \examples
* checking Rd metadata ... 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 data for ASCII and uncompressed saves ... WARNING
  Warning: package needs dependence on R (>= 2.10)
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘chopsticks/libs/chopsticks.so’:
  Found non-API call to R: ‘R_data_class’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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 WARNINGs, 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/chopsticks.Rcheck/00check.log’
for details.