• using R Under development (unstable) (2026-04-15 r89886)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)     GNU Fortran (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)
• running under: Fedora Linux 42 (Workstation Edition)
• using session charset: UTF-8 * current time: 2026-04-15 19:25:36 UTC
• using option ‘--no-stop-on-test-error’
• checking for file ‘ShortRead/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘ShortRead’ version ‘1.69.3-2’
• 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 executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘ShortRead’ can be installed ... [125s/318s] WARNING 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 the install log 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)’
• checking package directory ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... WARNING   Output from running autoreconf:   configure.ac:14: warning: The macro 'AC_ERROR' is obsolete.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’
• 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 ... [20s/80s] OK
• checking whether the package can be loaded with stated dependencies ... [17s/103s] OK
• checking whether the package can be unloaded cleanly ... [20s/32s] OK
• checking whether the namespace can be loaded with stated dependencies ... [19s/21s] OK
• checking whether the namespace can be unloaded cleanly ... [20s/24s] OK
• checking loading without being on the library search path ... [23s/26s] OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... NOTE Unexported object imported by a ':::' call: ‘S4Vectors:::V_recycle’   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 ... [110s/124s] 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
• checking Rd files ... NOTE checkRd: (-1) deprecated.Rd:21: Lost braces in \itemize; meant \describe ? checkRd: (-1) deprecated.Rd:23-24: Lost braces in \itemize; meant \describe ?
• checking Rd metadata ... OK
• checking Rd line widths ... 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 use of SHLIB_OPENMP_*FLAGS in Makefiles ... 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).
• checking pragmas in C/C++ headers and code ... OK
• checking compilation flags used ... OK
• checking compiled code ... WARNING 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.
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [71s/140s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [43s/101s] OK   Running ‘ShortRead_unit_tests.R’ [42s/99s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [45s/112s] OK
• checking PDF version of manual ... [17s/47s] OK
• checking HTML version of manual ... [18s/44s] OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 3 WARNINGs, 4 NOTEs