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### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:MANOR.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings MANOR_1.74.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/MANOR.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘MANOR/DESCRIPTION’ ... OK
* this is package ‘MANOR’ version ‘1.74.0’
* 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 whether package ‘MANOR’ can be installed ... WARNING
Found the following significant warnings:
  /usr/include/x86_64-linux-gnu/bits/string_fortified.h:95:10: warning: ‘__builtin_strncpy’ output may be truncated copying 100 bytes from a string of length 100 [-Wstringop-truncation]
See ‘/home/biocbuild/bbs-3.18-bioc/meat/MANOR.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* 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 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 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 ... WARNING
checkRd: (7) detectSB.Rd:47: Invalid email address: Philippe.Hupe@.curie.fr
checkRd: (-1) flag.summary.Rd:33: Escaped LaTeX specials: \$
checkRd: (-1) flag.summary.Rd:35: Escaped LaTeX specials: \$
checkRd: (-1) genome.plot.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) report.plot.Rd:22: Escaped LaTeX specials: \$
checkRd: (-1) report.plot.Rd:29: Escaped LaTeX specials: \$
* 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 C/C++/Fortran sources/headers ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.18-bioc/R/site-library/MANOR/libs/MANOR.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘MANOR.Rmd’ using ‘UTF-8’... failed
 ERROR
Errors in running code in vignettes:
when running code in ‘MANOR.Rmd’
  ...
> data(spatial)

> edge.norm$cloneValues$ZoneGNL <- as.factor(edge.norm$cloneValues$ZoneGNL)

> genome.plot(edge.norm, col.var = "ZoneGNL", chrLim = "LimitChr", 
+     cex = 1)

  When sourcing ‘MANOR.R’:
Error: figure margins too large
Execution halted

* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 3 WARNINGs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/MANOR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL MANOR
###
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* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘MANOR’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c Rnem_arg.c -o Rnem_arg.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c Rnem_exe.c -o Rnem_exe.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c exememo.c -o exememo.o
In file included from /home/biocbuild/bbs-3.18-bioc/R/include/R.h:73,
                 from exememo.c:20:
exememo.c: In function ‘GenAlloc’:
/home/biocbuild/bbs-3.18-bioc/R/include/R_ext/Error.h:64:15: warning: ‘msg’ may be used uninitialized [-Wmaybe-uninitialized]
   64 | #define error Rf_error
      |               ^~~~~~~~
exememo.c:39:11: note: ‘msg’ was declared here
   39 |     char* msg;
      |           ^~~
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c nem_alg.c -o nem_alg.o
In file included from /usr/include/string.h:535,
                 from nem_alg.c:72:
In function ‘strncpy’,
    inlined from ‘ClassifyByNemHeuBeta’ at nem_alg.c:801:7,
    inlined from ‘ClassifyByNem’ at nem_alg.c:578:13:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:95:10: warning: ‘__builtin_strncpy’ output may be truncated copying 100 bytes from a string of length 100 [-Wstringop-truncation]
   95 |   return __builtin___strncpy_chk (__dest, __src, __len,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   96 |                                   __glibc_objsize (__dest));
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c nem_hlp.c -o nem_hlp.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c nem_mod.c -o nem_mod.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c nem_nei.c -o nem_nei.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c nem_rnd.c -o nem_rnd.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c nem_ver.c -o nem_ver.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c registerDynamicSymbols.c -o registerDynamicSymbols.o
gcc -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o MANOR.so Rnem_arg.o Rnem_exe.o exememo.o nem_alg.o nem_hlp.o nem_mod.o nem_nei.o nem_rnd.o nem_ver.o registerDynamicSymbols.o -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.18-bioc/R/site-library/00LOCK-MANOR/00new/MANOR/libs
** R
** data
** 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 (MANOR)