CRAN Package Check Results for Maintainer ‘Bioconductor Package Maintainer <maintainer at bioconductor.org>’

Last updated on 2026-04-17 11:54:28 CEST.

Package	WARN
ShortRead	3

Package ShortRead

Current CRAN status:

Additional issues

gcc-ASAN linux-arm64

Version: 1.69.3-2
Check: CRAN incoming feasibility
Result: NOTE Maintainer: ‘Bioconductor Package Maintainer <maintainer@bioconductor.org>’ Package CITATION file contains call(s) to old-style personList() or as.personList(). Please use c() on person objects instead. Package CITATION file contains call(s) to old-style citEntry(). Please use bibentry() instead. Found the following (possibly) invalid file URIs: URI: cwon2@fhcrc.org From: man/SpTrellis-class.Rd URI: mtmorgan@fhcrc.org From: man/filterFastq.Rd Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.69.3-2
Check: whether package can be installed
Result: WARN Found the following significant warnings: io.c:227:38: warning: format ‘%f’ expects argument of type ‘double’, but argument 2 has type ‘const char *’ [-Wformat=] io.c:658:49: warning: format ‘%s’ expects argument of type ‘char *’, but argument 2 has type ‘int’ [-Wformat=] io.c:676:48: warning: format ‘%s’ expects argument of type ‘char *’, but argument 2 has type ‘int’ [-Wformat=] readBfaToc.cc:36:19: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] readBfaToc.cc:37:19: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] readBfaToc.cc:38:19: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] maqmap_m.h:102:21: warning: pointer ‘mm’ used after ‘void free(void*)’ [-Wuse-after-free] See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ShortRead.Rcheck/00install.out’ for details. * used C compiler: ‘gcc-15 (Debian 15.2.0-16) 15.2.0’ * used C++ compiler: ‘g++-15 (Debian 15.2.0-16) 15.2.0’ Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.69.3-2
Check: top-level files
Result: WARN Output from running autoreconf: configure.ac:14: warning: The macro 'AC_ERROR' is obsolete. configure.ac:14: You should run autoupdate. ./lib/autoconf/oldnames.m4:34: AC_ERROR is expanded from... configure.ac:14: the top level configure.ac:17: warning: AC_OUTPUT should be used without arguments. configure.ac:17: You should run autoupdate. Non-standard file/directory found at top level: ‘issue-10.R’ Flavors: r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.69.3-2
Check: dependencies in R code
Result: NOTE Unexported object imported by a ':::' call: ‘S4Vectors:::V_recycle’ See the note in ?`:::` about the use of this operator. Flavors: r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.69.3-2
Check: R code for possible problems
Result: NOTE .plotCycleBaseCall: no visible binding for global variable ‘Base’ flag,QAReadQuality: no visible binding for global variable ‘Score’ flag,QAReadQuality: no visible binding for global variable ‘Id’ flag,QAReadQuality: no visible binding for global variable ‘Density’ report,QAFrequentSequence: no visible binding for global variable ‘TopCount’ report,QAFrequentSequence: no visible binding for global variable ‘Id’ report,QANucleotideByCycle: no visible binding for global variable ‘Base’ report,QANucleotideUse: no visible binding for global variable ‘Nucleotide’ report,QAQualityUse: no visible binding for global variable ‘Count’ report,QAQualityUse: no visible binding for global variable ‘Id’ report,QAQualityUse: no visible binding for global variable ‘Quality’ report,QAReadQuality: no visible binding for global variable ‘Id’ report,QASequenceUse: no visible binding for global variable ‘Occurrences’ report,QASequenceUse: no visible binding for global variable ‘Id’ report,QASequenceUse: no visible binding for global variable ‘Reads’ trimEnds,XStringSet: no visible global function definition for ‘seqtype’ Undefined global functions or variables: Base Count Density Id Nucleotide Occurrences Quality Reads Score TopCount seqtype Flavors: r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.69.3-2
Check: Rd files
Result: NOTE checkRd: (-1) deprecated.Rd:21: Lost braces in \itemize; meant \describe ? checkRd: (-1) deprecated.Rd:23-24: Lost braces in \itemize; meant \describe ? Flavors: r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.69.3-2
Check: Rd cross-references
Result: NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: SRSet-class.Rd: phenoData-class Sampler-class.Rd: IRanges-class ShortRead-class.Rd: writeXStringSet Snapshot-class.Rd: GRanges qa.Rd: BiocParallelParam qa2.Rd: matchPattern readBfaToc.Rd: coverage readFasta.Rd: writeXStringSet, DNAStringSet-class Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.69.3-2
Check: use of SHLIB_OPENMP_*FLAGS in Makefiles
Result: NOTE src/Makevars.in: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++ Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R Extensions’. The macros for different languages may differ so the matching macro must be used in PKG_CXXFLAGS (etc) and match that used in PKG_LIBS (except for Fortran: see the manual). Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.69.3-2
Check: compiled code
Result: WARN File ‘ShortRead/libs/ShortRead.so’: Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C) Object: ‘xsnap.o’ File ‘ShortRead/libs/ShortRead.so’: Found non-API call to R: ‘Rf_findVar’ This entry point may be removed soon. 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. Compiled code should not call non-API entry points in R. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual, and section ‘Moving into C API compliance’ for issues with the use of non-API entry points. Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.69.3-2
Check: whether package can be installed
Result: WARN Found the following significant warnings: io.c:227:43: warning: format specifies type 'double' but the argument has type 'const char *' [-Wformat] io.c:659:23: warning: format specifies type 'char *' but the argument has type 'char' [-Wformat] io.c:677:19: warning: format specifies type 'char *' but the argument has type 'char' [-Wformat] See ‘/data/gannet/ripley/R/packages/tests-clang/ShortRead.Rcheck/00install.out’ for details. * used C compiler: ‘clang version 22.1.3 (https://github.com/llvm/llvm-project e9846648fd6183ee6d8cbdb4502213fcf902a211)’ * used C++ compiler: ‘clang version 22.1.3 (https://github.com/llvm/llvm-project e9846648fd6183ee6d8cbdb4502213fcf902a211)’ Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.69.3-2
Check: use of SHLIB_OPENMP_*FLAGS in Makefiles
Result: NOTE src/Makevars: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++ src/Makevars.in: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++ Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R Extensions’. The macros for different languages may differ so the matching macro must be used in PKG_CXXFLAGS (etc) and match that used in PKG_LIBS (except for Fortran: see the manual). Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.69.3-2
Check: compiled code
Result: WARN File ‘ShortRead/libs/ShortRead.so’: Found ‘__vsprintf_chk’, possibly from ‘vsprintf’ (C) Object: ‘xsnap.o’ File ‘ShortRead/libs/ShortRead.so’: Found non-API call to R: ‘Rf_findVar’ File ‘ShortRead/libs/ShortRead.so’: Found no call to: ‘R_useDynamicSymbols’ This entry point may be removed soon. 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. Compiled code should not call non-API entry points in R. It is good practice to register native routines and to disable symbol search. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual, and section ‘Moving into C API compliance’ for issues with the use of non-API entry points. Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.69.3-2
Check: whether package can be installed
Result: WARN Found the following significant warnings: io.c:227:38: warning: format ‘%f’ expects argument of type ‘double’, but argument 2 has type ‘const char *’ [-Wformat=] io.c:658:49: warning: format ‘%s’ expects argument of type ‘char *’, but argument 2 has type ‘int’ [-Wformat=] io.c:676:48: warning: format ‘%s’ expects argument of type ‘char *’, but argument 2 has type ‘int’ [-Wformat=] maqmap_m.h:102:21: warning: pointer ‘mm’ used after ‘void free(void*)’ [-Wuse-after-free] readBfaToc.cc:36:19: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] readBfaToc.cc:37:19: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] readBfaToc.cc:38:19: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] See ‘/data/gannet/ripley/R/packages/tests-devel/ShortRead.Rcheck/00install.out’ for details. * used C compiler: ‘gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’ * used C++ compiler: ‘g++ (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’ Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 1.69.3-2
Check: compiled code
Result: WARN File ‘ShortRead/libs/ShortRead.so’: Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C) Object: ‘xsnap.o’ File ‘ShortRead/libs/ShortRead.so’: Found non-API call to R: ‘Rf_findVar’ File ‘ShortRead/libs/ShortRead.so’: Found no call to: ‘R_useDynamicSymbols’ This entry point may be removed soon. 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. Compiled code should not call non-API entry points in R. It is good practice to register native routines and to disable symbol search. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual, and section ‘Moving into C API compliance’ for issues with the use of non-API entry points. Flavor: r-devel-linux-x86_64-fedora-gcc