Last updated on 2026-04-18 17:51:22 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.69.3-2 | 70.51 | 426.99 | 497.50 | WARN | |
| r-devel-linux-x86_64-debian-gcc | 1.69.3-2 | 49.14 | 307.79 | 356.93 | WARN | |
| r-devel-linux-x86_64-fedora-clang | 1.69.3-2 | 117.00 | 692.84 | 809.84 | WARN | |
| r-devel-linux-x86_64-fedora-gcc | 1.69.3-2 | 116.00 | 675.69 | 791.69 | WARN |
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
Flavors: r-devel-linux-x86_64-debian-clang, 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 ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ShortRead.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 21.1.8 (3+b1)’
* used C++ compiler: ‘Debian clang version 21.1.8 (3+b1)’
Flavor: r-devel-linux-x86_64-debian-clang
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configure.ac:14: warning: The macro 'AC_ERROR' is obsolete.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-clang, 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-clang, 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-clang, 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-clang, 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.
Flavors: r-devel-linux-x86_64-debian-clang, 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).
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-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’
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-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=]
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: 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=]
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 ‘/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