##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:GLAD.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings GLAD_2.71.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/GLAD.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘GLAD/DESCRIPTION’ ... OK
* this is package ‘GLAD’ version ‘2.71.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘GLAD’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
* used C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
* checking installed package size ... OK
* checking package directory ... 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 code 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... WARNING
Missing or unexported object: ‘aws::laws’
* 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 ... WARNING
checkRd: (5) as.profileCGH.Rd:25: \item in \value must have non-empty label
checkRd: (-1) daglad.Rd:47: Escaped LaTeX specials: \$
checkRd: (5) daglad.Rd:182-183: \item in \value must have non-empty label
checkRd: (-1) daglad.Rd:192-193: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) daglad.Rd:196-199: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) daglad.Rd:202-205: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) daglad.Rd:207-210: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) daglad.Rd:213-216: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) daglad.Rd:218: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) daglad.Rd:221-224: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) daglad.Rd:226-228: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) daglad.Rd:240: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) daglad.Rd:241: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) daglad.Rd:242-243: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) daglad.Rd:244: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) daglad.Rd:245: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) daglad.Rd:246: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) daglad.Rd:247-248: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) daglad.Rd:249: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (5) glad.Rd:152: \item in \value must have non-empty label
checkRd: (-1) glad.Rd:159-160: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glad.Rd:162-165: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glad.Rd:168-171: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glad.Rd:173-176: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glad.Rd:178-179: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glad.Rd:182-185: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glad.Rd:187: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glad.Rd:189-190: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glad.Rd:192-193: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glad.Rd:195-196: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glad.Rd:204: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glad.Rd:205: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glad.Rd:206: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glad.Rd:213: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glad.Rd:214: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glad.Rd:224: Lost braces in \itemize; meant \describe ?
checkRd: (-1) glad.Rd:225: Lost braces in \itemize; meant \describe ?
checkRd: (-1) glad.Rd:226: Lost braces in \itemize; meant \describe ?
* 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 ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.21-bioc/R/site-library/GLAD/libs/GLAD.so’:
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
  Found ‘__printf_chk’, possibly from ‘printf’ (C)
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/GLAD.Rcheck/00check.log’
for details.