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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:msa.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings msa_1.38.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/msa.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘msa/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘msa’ version ‘1.38.0’
* 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 ‘msa’ can be installed ... WARNING
Found the following significant warnings:
  alpha.cpp:84:16: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch]
  clust.cpp:167:16: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch]
  clust.cpp:295:16: warning: enumeration value 'LINKAGE_Undefined' not handled in switch [-Wswitch]
  clust.cpp:611:16: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch]
  glbalndimer.cpp:123:16: warning: enumeration value 'PPSCORE_Undefined' not handled in switch [-Wswitch]
  glbalndimer.cpp:123:16: warning: enumeration value 'PPSCORE_SPN' not handled in switch [-Wswitch]
  msa2.cpp:357:16: warning: enumeration value 'SEQWEIGHT_Undefined' not handled in switch [-Wswitch]
  objscore.cpp:31:16: warning: enumeration value 'OBJSCORE_Undefined' not handled in switch [-Wswitch]
  objscore.cpp:31:16: warning: enumeration value 'OBJSCORE_SPM' not handled in switch [-Wswitch]
  objscore2.cpp:22:16: warning: enumeration value 'TERMGAPS_Undefined' not handled in switch [-Wswitch]
  params.cpp:441:16: warning: enumeration value 'PPSCORE_Undefined' not handled in switch [-Wswitch]
  msadist.h:22:23: warning: enumeration value 'DISTANCE_Undefined' not handled in switch [-Wswitch]
  msadist.h:22:23: warning: enumeration value 'DISTANCE_Kmer6_6' not handled in switch [-Wswitch]
  msadist.h:22:23: warning: enumeration value 'DISTANCE_Kmer20_3' not handled in switch [-Wswitch]
  msadist.h:22:23: warning: enumeration value 'DISTANCE_Kmer20_4' not handled in switch [-Wswitch]
  msadist.h:22:23: warning: enumeration value 'DISTANCE_Kbit20_3' not handled in switch [-Wswitch]
  msadist.h:22:23: warning: enumeration value 'DISTANCE_Kmer4_6' not handled in switch [-Wswitch]
  msadist.h:22:23: warning: enumeration value 'DISTANCE_PWKimura' not handled in switch [-Wswitch]
  msadist.h:22:23: warning: enumeration value 'DISTANCE_PWScoreDist' not handled in switch [-Wswitch]
  msadist.h:22:23: warning: enumeration value 'DISTANCE_ScoreDist' not handled in switch [-Wswitch]
  msadist.h:22:23: warning: enumeration value 'DISTANCE_Edit' not handled in switch [-Wswitch]
  profilefrommsa.cpp:230:16: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch]
  fileInput/FileReader.cpp:692:21: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=]
  alignment/AlignmentOutput.cpp:683:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=]
  alignment/AlignmentOutput.cpp:878:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=]
  alignment/AlignmentOutput.cpp:1037:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=]
  alignment/AlignmentOutput.cpp:1166:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=]
  alignment/AlignmentOutput.cpp:1455:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=]
  alignment/AlignmentOutput.cpp:1570:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=]
  alignment/AlignmentOutput.cpp:2153:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=]
  alignment/AlignmentOutput.cpp:2160:21: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=]
  alignment/AlignmentOutput.cpp:2410:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=]
  argtable2/argtable2.c:590:10: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  squid/ssi.c:751:26: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'long long unsigned int' [-Wformat=]
  squid/ssi.c:751:26: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'long long unsigned int' [-Wformat=]
  squid/ssi.c:1407:24: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'long long unsigned int' [-Wformat=]
  squid/ssi.c:1407:24: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'long long unsigned int' [-Wformat=]
  hhalign/hhhitlist-C.h:663:9: warning: the address of 'HMM::fam' will never be NULL [-Waddress]
  hhalign/hhhitlist-C.h:840:9: warning: the address of 'HMM::fam' will never be NULL [-Waddress]
  hhalign/hhhmm-C.h:294:20: warning: 'char* strncat(char*, const char*, size_t)' output may be truncated copying between 0 and 510 bytes from a string of length 262139 [-Wstringop-truncation]
  hhalign/hhhmm-C.h:285:27: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 254 bytes from a string of length 262140 [-Wstringop-truncation]
  hhalign/hhhmm-C.h:269:22: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 32764 bytes from a string of length 262139 [-Wstringop-truncation]
  hhalign/hhhmm-C.h:668:18: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 510 bytes from a string of length 262139 [-Wstringop-truncation]
  hhalign/hhhmm-C.h:684:22: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 32764 bytes from a string of length 262139 [-Wstringop-truncation]
  hhalign/hhhmm-C.h:676:18: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 32764 bytes from a string of length 262139 [-Wstringop-truncation]
  hhalign/hhhmm-C.h:1006:10: warning: 'char* strncat(char*, const char*, size_t)' output may be truncated copying between 0 and 32764 bytes from a string of length 32764 [-Wstringop-truncation]
  hhalign/hhhmm-C.h:1167:25: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 510 bytes from a string of length 262139 [-Wstringop-truncation]
  hhalign/hhhmm-C.h:1183:33: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 32764 bytes from a string of length 262139 [-Wstringop-truncation]
  hhalign/hhhmm-C.h:1175:25: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 32764 bytes from a string of length 262139 [-Wstringop-truncation]
  hhalign/hhhmm-C.h:1500:9: warning: 'char* strncat(char*, const char*, size_t)' output may be truncated copying between 0 and 32764 bytes from a string of length 32764 [-Wstringop-truncation]
  hhalign/hhhmm-C.h:1748:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  hhalign/hhalignment-C.h:247:26: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 32764 bytes from a string of length 262142 [-Wstringop-truncation]
See ‘/home/biocbuild/bbs-3.20-bioc/meat/msa.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’
* used C compiler: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’
* checking installed package size ... NOTE
  installed size is 26.6Mb
  sub-directories of 1Mb or more:
    libs  25.4Mb
* 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 ... 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 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 include directives in Makefiles ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/R/R-4.4.1/site-library/msa/libs/msa.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘printf’, possibly from ‘printf’ (C)
  Found ‘putchar’, possibly from ‘putchar’ (C)
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘sprintf’, possibly from ‘sprintf’ (C)
  Found ‘srand’, possibly from ‘srand’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
  Found ‘vsprintf’, possibly from ‘vsprintf’ (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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

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