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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:mosaics.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings mosaics_2.37.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/mosaics.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘mosaics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mosaics’ version ‘2.37.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘mosaics’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* 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 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 ... WARNING
Error in library(mosaics, lib.loc = "/home/biocbuild/bbs-3.17-bioc/R/library") : 
  there is no package called ‘mosaics’
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
* 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 ... OK
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... SKIPPED
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘mosaics-example.Rnw’... failed to complete the test
 ERROR
Errors in running code in vignettes:
when running code in ‘mosaics-example.Rnw’
  ...
Info: Loading and processing ChIP sample file...
Info: Single-end tag (SET) is assumed (PET=FALSE).
Info: Average fragment length is set as 200 (fragLen=200).
Info: Use the provided BAM index file.
Info: Reading and processing aligned read file...
Info: Processing and combining peak list and reads...
Info: Calculating coverage...
Killed

... incomplete output.  Crash?

* checking re-building of vignette outputs ... NOTE
Error(s) in re-building vignettes:
--- re-building ‘mosaics-example.Rnw’ using Sweave
Loading required package: Rcpp
Use the provided BAM index file.
Chromosome information is extracted from the BAM file.
Info: reading the aligned read file and processing it into bin-level files...
Info: done!
Use the provided BAM index file.
Chromosome information is extracted from the BAM file.
Info: reading the aligned read file and processing it into bin-level files...
Info: done!
Info: reading and preprocessing bin-level data...
Info: data contains only one chromosome.
Info: done!

Info: background estimation based on robust method of moment.
Info: two-sample analysis (Input only).
Info: use adaptive griding.
Info: fitting background model...
Warning in rlm.default(x, y, weights, method = method, wt.method = wt.method,  :
  'rlm' failed to converge in 20 steps
Info: done!
Info: fitting one-signal-component model...
Info: fitting two-signal-component model...
Info: calculating BIC of fitted models...
Info: done!
Info: use two-signal-component model.
Info: calculating posterior probabilities...
Info: calling peaks...
Info: done!
Use the provided BAM index file.
Info: done!
Use the provided BAM index file.
Chromosome information is extracted from the BAM file.
Info: reading the aligned read file and processing it into bin-level files...
Info: done!
Use the provided BAM index file.
Chromosome information is extracted from the BAM file.
Info: reading the aligned read file and processing it into bin-level files...
Info: done!
Info: reading and preprocessing bin-level data...
Info: data contains only one chromosome.
Info: done!

Info: background estimation based on robust method of moment.
Info: two-sample analysis (Input only).
Info: use adaptive griding.
Info: fitting background model...
Warning in rlm.default(x, y, weights, method = method, wt.method = wt.method,  :
  'rlm' failed to converge in 20 steps
Info: done!
Info: fitting one-signal-component model...
Info: fitting two-signal-component model...
Info: calculating BIC of fitted models...
Info: done!
Info: initialize MOSAiCS-HMM using MOSAiCS peak calling results.
Info: use two-signal-component model.
Info: initializing HMM parameters...
Info: estimating HMM parameters...
Info: calculating BIC of fitted models...
Info: done!
Info: summarizing ChIP-seq data...
Info: simulating background tags...
Info: simulating ChIP tags for MOSAiCS...
Info: simulating ChIP tags for MOSAiCS-HMM...
Info: peak calling using posterior decoding.
Info: calculating posterior probabilities...
Info: calling peaks...
Killed

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/mosaics.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL mosaics
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘mosaics’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c convolution_1S.cpp -o convolution_1S.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c convolution_2S.cpp -o convolution_2S.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c emHMM.cpp -o emHMM.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c stack.cpp -o stack.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c updatePiMat.cpp -o updatePiMat.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c viterbi.cpp -o viterbi.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o mosaics.so convolution_1S.o convolution_2S.o emHMM.o stack.o updatePiMat.o viterbi.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-mosaics/00new/mosaics/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (mosaics)