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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:MANOR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings MANOR_1.78.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/MANOR.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 ‘MANOR/DESCRIPTION’ ... OK
* this is package ‘MANOR’ version ‘1.78.0’
* package encoding: UTF-8
* 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 ‘MANOR’ can be installed ... WARNING
Found the following significant warnings:
  exememo.c:43:7: warning: format not a string literal and no format arguments [-Wformat-security]
  nem_alg.c:801:7: warning: ‘__builtin_strncpy’ output may be truncated copying 100 bytes from a string of length 100 [-Wstringop-truncation]
See ‘/home/biocbuild/bbs-3.20-bioc/meat/MANOR.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (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 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
checkRd: (-1) genome.plot.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) spatial.Rd:33-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spatial.Rd:41: 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 C/C++/Fortran sources/headers ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.20-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 ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/MANOR.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL MANOR
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘MANOR’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
gcc -I"/home/biocbuild/bbs-3.20-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-3.20-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-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c exememo.c -o exememo.o
exememo.c: In function ‘GenAlloc’:
exememo.c:43:7: warning: format not a string literal and no format arguments [-Wformat-security]
   43 |       error(msg);
      |       ^~~~~
In file included from /usr/include/stdio.h:980,
                 from exememo.c:19:
In function ‘sprintf’,
    inlined from ‘GenAlloc’ at exememo.c:40:5:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: warning: ‘msg’ may be used uninitialized [-Wmaybe-uninitialized]
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
exememo.c: In function ‘GenAlloc’:
exememo.c:39:11: note: ‘msg’ was declared here
   39 |     char* msg;
      |           ^~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c nem_alg.c -o nem_alg.o
nem_alg.c: In function ‘ClassifyByNem’:
nem_alg.c:801:7: warning: ‘__builtin_strncpy’ output may be truncated copying 100 bytes from a string of length 100 [-Wstringop-truncation]
  801 |       strncpy( namecri, NemParaP->OutBaseName, LEN_FILENAME ) ;
      |       ^
gcc -I"/home/biocbuild/bbs-3.20-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-3.20-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-3.20-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-3.20-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-3.20-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-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c registerDynamicSymbols.c -o registerDynamicSymbols.o
gcc -shared -L/home/biocbuild/bbs-3.20-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-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-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)