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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:gmapR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings gmapR_1.49.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/gmapR.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gmapR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gmapR’ version ‘1.49.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... WARNING
Found the following files with non-portable file names:
  src/gmap/config/lt~obsolete.m4
  src/gstruct/config/lt~obsolete.m4
These are not fully portable file names.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘gmapR’ can be installed ... WARNING
Found the following significant warnings:
  WARNING: You don't seem to have gsnap specified.
  samtools/bam.c:128:9: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
  samtools/razf.c:178:9: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
  access.c:59:7: warning: implicit declaration of function ‘stat64’; did you mean ‘stat’? [-Wimplicit-function-declaration]
  md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=]
  access.c:61:7: warning: implicit declaration of function ‘stat64’; did you mean ‘stat’? [-Wimplicit-function-declaration]
  gmap.c:3244:70: warning: passing argument 11 of ‘check_middle_piece_local’ from incompatible pointer type [-Wincompatible-pointer-types]
  gmap.c:3244:79: warning: passing argument 12 of ‘check_middle_piece_local’ from incompatible pointer type [-Wincompatible-pointer-types]
  table.c:283:18: warning: passing argument 1 of ‘keyfree’ from incompatible pointer type [-Wincompatible-pointer-types]
  sarray-read.c:302:22: warning: assignment to ‘UINT4 *’ {aka ‘unsigned int *’} from incompatible pointer type ‘Univcoord_T *’ {aka ‘long long unsigned int *’} [-Wincompatible-pointer-types]
  sarray-read.c:368:22: warning: assignment to ‘UINT4 *’ {aka ‘unsigned int *’} from incompatible pointer type ‘Univcoord_T *’ {aka ‘long long unsigned int *’} [-Wincompatible-pointer-types]
  sarray-read.c:434:22: warning: assignment to ‘UINT4 *’ {aka ‘unsigned int *’} from incompatible pointer type ‘Univcoord_T *’ {aka ‘long long unsigned int *’} [-Wincompatible-pointer-types]
  sarray-read.c:526:22: warning: assignment to ‘UINT4 *’ {aka ‘unsigned int *’} from incompatible pointer type ‘Univcoord_T *’ {aka ‘long long unsigned int *’} [-Wincompatible-pointer-types]
  sarray-read.c:653:22: warning: assignment to ‘UINT4 *’ {aka ‘unsigned int *’} from incompatible pointer type ‘Univcoord_T *’ {aka ‘long long unsigned int *’} [-Wincompatible-pointer-types]
  sarray-read.c:2170:11: warning: assignment to ‘Univcoord_T *’ {aka ‘long long unsigned int *’} from incompatible pointer type ‘UINT4 *’ {aka ‘unsigned int *’} [-Wincompatible-pointer-types]
  sarray-read.c:2442:44: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types]
  sarray-read.c:2442:27: warning: assignment to ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} from incompatible pointer type ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} [-Wincompatible-pointer-types]
  sarray-read.c:2456:97: warning: passing argument 12 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types]
  sarray-read.c:2499:44: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types]
  sarray-read.c:2499:27: warning: assignment to ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} from incompatible pointer type ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} [-Wincompatible-pointer-types]
  sarray-read.c:2513:73: warning: passing argument 11 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types]
  sarray-read.c:2643:44: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types]
  sarray-read.c:2643:27: warning: assignment to ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} from incompatible pointer type ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} [-Wincompatible-pointer-types]
  sarray-read.c:2656:113: warning: passing argument 12 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types]
  sarray-read.c:2699:44: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types]
  sarray-read.c:2699:27: warning: assignment to ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} from incompatible pointer type ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} [-Wincompatible-pointer-types]
  sarray-read.c:2712:89: warning: passing argument 11 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types]
  sarray-read.c:2752:11: warning: assignment to ‘Univcoord_T *’ {aka ‘long long unsigned int *’} from incompatible pointer type ‘UINT4 *’ {aka ‘unsigned int *’} [-Wincompatible-pointer-types]
  sarray-read.c:3024:44: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types]
  sarray-read.c:3024:27: warning: assignment to ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} from incompatible pointer type ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} [-Wincompatible-pointer-types]
  sarray-read.c:3038:97: warning: passing argument 12 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types]
  sarray-read.c:3082:44: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types]
  sarray-read.c:3082:27: warning: assignment to ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} from incompatible pointer type ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} [-Wincompatible-pointer-types]
  sarray-read.c:3096:73: warning: passing argument 11 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types]
  sarray-read.c:3217:44: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types]
  sarray-read.c:3217:27: warning: assignment to ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} from incompatible pointer type ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} [-Wincompatible-pointer-types]
  sarray-read.c:3231:97: warning: passing argument 12 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types]
  sarray-read.c:3274:44: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types]
  sarray-read.c:3274:27: warning: assignment to ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} from incompatible pointer type ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} [-Wincompatible-pointer-types]
  sarray-read.c:3288:73: warning: passing argument 11 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types]
See ‘/home/biocbuild/bbs-3.21-bioc/meat/gmapR.Rcheck/00install.out’ for details.
* checking installed package size ... INFO
  installed size is 80.6Mb
  sub-directories of 1Mb or more:
    R         1.4Mb
    extdata   5.6Mb
    libs      1.9Mb
    usr      71.6Mb
* 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 ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    Initial release
    (start date: 12 September, 2012)
* 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 ... WARNING
'::' or ':::' import not declared from: ‘AnnotationDbi’
Unexported objects imported by ':::' calls:
  ‘BiocGenerics:::testPackage’ ‘S4Vectors:::labeledLine’
  ‘S4Vectors:::new_SimpleList_from_list’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
checkTallyConsistency: no visible binding for global variable
  ‘count.plus’
checkTallyConsistency: no visible binding for global variable
  ‘count.minus’
checkTallyConsistency: no visible binding for global variable
  ‘count.plus.ref’
checkTallyConsistency: no visible binding for global variable
  ‘count.minus.ref’
fieldNames: no visible global function definition for
  ‘R_iit_fieldNames’
newGmapAlignerParam: ... may be used in an incorrect context:
  ‘list(...)’
open.IITFile: no visible binding for global variable ‘R_iit_read’
open.IITFile: no visible global function definition for ‘resource’
typeNames: no visible global function definition for ‘R_iit_typeNames’
variantSummary: no visible binding for global variable ‘count.total’
variantSummary: no visible binding for global variable ‘count.ref’
variantSummary: no visible binding for global variable ‘count’
import,IITFile-ANY-ANY: no visible global function definition for
  ‘checkArgFormat’
import,IITFile-ANY-ANY: no visible binding for global variable
  ‘R_iit_read’
snps<-,GmapSnpDirectory-character-VCF: no visible global function
  definition for ‘rowData’
Undefined global functions or variables:
  R_iit_fieldNames R_iit_read R_iit_typeNames checkArgFormat count
  count.minus count.minus.ref count.plus count.plus.ref count.ref
  count.total resource rowData
* checking Rd files ... WARNING
checkRd: (5) GmapGenome-class.Rd:30-56: \item in \describe must have non-empty label
checkRd: (5) GmapGenome-class.Rd:62-67: \item in \describe must have non-empty label
checkRd: (5) GmapGenome-class.Rd:73-77: \item in \describe must have non-empty label
checkRd: (5) GmapGenome-class.Rd:83-85: \item in \describe must have non-empty label
checkRd: (5) GmapGenome-class.Rd:86-89: \item in \describe must have non-empty label
checkRd: (5) GmapGenome-class.Rd:90: \item in \describe must have non-empty label
checkRd: (5) GmapGenome-class.Rd:91-93: \item in \describe must have non-empty label
checkRd: (5) GmapGenomeDirectory-class.Rd:24-28: \item in \describe must have non-empty label
checkRd: (5) GmapGenomeDirectory-class.Rd:33: \item in \describe must have non-empty label
checkRd: (5) GmapGenomeDirectory-class.Rd:34-35: \item in \describe must have non-empty label
checkRd: (5) GmapSnps-class.Rd:35: \item in \describe must have non-empty label
checkRd: (5) GmapSnps-class.Rd:36-38: \item in \describe must have non-empty label
checkRd: (5) GsnapOutput-class.Rd:24-30: \item in \describe must have non-empty label
checkRd: (5) GsnapOutput-class.Rd:31-36: \item in \describe must have non-empty label
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘GmapParam’ ‘gmap’
Undocumented S4 classes:
  ‘GmapParam’ ‘GmapAlignerParam’
Undocumented S4 methods:
  generic 'as.character' and siglist 'GmapGenomeDirectory'
  generic 'bamPaths' and siglist 'GmapAlignerOutput'
  generic 'gmap' and siglist 'ANY,GmapParam'
  generic 'gmap' and siglist 'FastaFile,GmapParam'
  generic 'gmap' and siglist 'character,GmapParam'
  generic 'path' and siglist 'GmapAlignerOutput'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... WARNING
Found the following file(s) containing GNU extensions:
  src/Makefile
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif, .NOTPARALLEL See section ‘Writing portable
packages’ in the ‘Writing R Extensions’ manual.
* 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-4.5.0-devel_2024-11-24/site-library/gmapR/libs/gmapR.so’:
  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 ‘sprintf’, possibly from ‘sprintf’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (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 ‘tests’ ... OK
* checking tests ...
  Running ‘gmapR_unit_tests.R’
 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: 7 WARNINGs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/gmapR.Rcheck/00check.log’
for details.