Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-10-19 11:53 -0400 (Sat, 19 Oct 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4474 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4733 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4479 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4509 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4457 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 1937/2273 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SICtools 1.35.0 (landing page) Xiaobin Xing
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the SICtools package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SICtools.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: SICtools |
Version: 1.35.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:SICtools.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SICtools_1.35.0.tar.gz |
StartedAt: 2024-10-19 09:50:34 -0000 (Sat, 19 Oct 2024) |
EndedAt: 2024-10-19 09:52:49 -0000 (Sat, 19 Oct 2024) |
EllapsedTime: 135.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: SICtools.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:SICtools.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SICtools_1.35.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/SICtools.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 ‘SICtools/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SICtools’ version ‘1.35.0’ * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'Rsamtools', 'doParallel', 'Biostrings', 'stringr', 'matrixStats', 'plyr', 'GenomicRanges', 'IRanges' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘SICtools’ can be installed ... WARNING Found the following significant warnings: bam.c:128:2: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation] bam_index.c:178:35: warning: overflow in conversion from ‘uint32_t’ {aka ‘unsigned int’} to ‘int32_t’ {aka ‘int’} changes value from ‘last_bin = 4294967295’ to ‘-1’ [-Woverflow] razf.c:178:2: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation] errmod.c:79:8: warning: self-comparison always evaluates to false [-Wtautological-compare] md5.c:155:26: warning: argument to ‘sizeof’ in ‘memset’ call is the same expression as the destination; did you mean to dereference it? [-Wsizeof-pointer-memaccess] Warning: replacing previous import ‘plyr::count’ by ‘matrixStats::count’ when loading ‘SICtools’ See ‘/home/biocbuild/bbs-3.20-bioc/meat/SICtools.Rcheck/00install.out’ for details. * checking installed package size ... OK * 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: FEATURES Cannot process chunk/lines: This package is to find SNV/Indel differences between two bam files with near relationship Cannot process chunk/lines: in a way of pairwise comparison thourgh each base position across the genome region of interest. Cannot process chunk/lines: The difference is inferred by fisher test and euclidean distance, the input of which is the base Cannot process chunk/lines: count (A,T,G,C) in a given position and read counts for indels that span no less than 2bp on both Cannot process chunk/lines: sides of indel region. * 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 ... NOTE .indelDiffFunc: no visible global function definition for ‘fisher.test’ .indelDiffFunc: no visible global function definition for ‘dist’ indelDiff: no visible global function definition for ‘read.delim’ snpDiff : calcInfoRange : <anonymous>: no visible global function definition for ‘fisher.test’ snpDiff : calcInfoRange : <anonymous>: no visible global function definition for ‘dist’ Undefined global functions or variables: dist fisher.test read.delim Consider adding importFrom("stats", "dist", "fisher.test") importFrom("utils", "read.delim") to your NAMESPACE file. * 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 C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... 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 ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.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: 1 WARNING, 4 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/SICtools.Rcheck/00check.log’ for details.
SICtools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL SICtools ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘SICtools’ ... ** using staged installation ** libs Makefile:24: warning: overriding recipe for target '.c.o' /home/biocbuild/R/R-4.4.1/etc/Makeconf:195: warning: ignoring old recipe for target '.c.o' make[1]: Entering directory '/home/biocbuild/bbs-3.20-bioc/meat/SICtools/src' make[2]: Entering directory '/home/biocbuild/bbs-3.20-bioc/meat/SICtools/src' gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o bgzf.c: In function ‘worker_aux’: bgzf.c:392:9: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable] 392 | int i, tmp, stop = 0; | ^~~ bgzf.c: In function ‘bgzf_close’: bgzf.c:572:11: warning: variable ‘count’ set but not used [-Wunused-but-set-variable] 572 | int ret, count, block_length; | ^~~~~ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o bam.c: In function ‘bam_header_write’: bam.c:128:2: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation] 128 | strncpy(buf, "BAM\001", 4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o bam_index.c: In function ‘bam_index_core’: bam_index.c:178:35: warning: overflow in conversion from ‘uint32_t’ {aka ‘unsigned int’} to ‘int32_t’ {aka ‘int’} changes value from ‘last_bin = 4294967295’ to ‘-1’ [-Woverflow] 178 | save_bin = save_tid = last_tid = last_bin = 0xffffffffu; | ^~~~~~~~ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o bam_pileup.c: In function ‘resolve_cigar2’: bam_pileup.c:75:9: warning: variable ‘is_head’ set but not used [-Wunused-but-set-variable] 75 | int k, is_head = 0; | ^~~~~~~ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o razf.c: In function ‘razf_open_w’: razf.c:178:2: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation] 178 | strncpy((char*)rz->header->extra, "RAZF", 4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o faidx.c: In function ‘fai_load’: faidx.c:277:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 277 | else | ^~~~ faidx.c:280:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 280 | if (fp == 0) { | ^~ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o bam_reheader.c: In function ‘bam_reheader’: bam_reheader.c:12:16: warning: variable ‘old’ set but not used [-Wunused-but-set-variable] 12 | bam_header_t *old; | ^~~ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o kprobaln.c: In function ‘kpa_glocal’: kprobaln.c:78:21: warning: variable ‘is_diff’ set but not used [-Wunused-but-set-variable] 78 | int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr; | ^~~~~~~ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o make[2]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/SICtools/src' make[2]: Entering directory '/home/biocbuild/bbs-3.20-bioc/meat/SICtools/src/bcftools' gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o bcf.c: In function ‘bcf_fmt_core’: bcf.c:233:9: warning: variable ‘iPL’ set but not used [-Wunused-but-set-variable] 233 | int iPL = -1; | ^~~ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o bcfutils.c: In function ‘bcf_fit_alt’: bcfutils.c:119:9: warning: variable ‘ipl’ set but not used [-Wunused-but-set-variable] 119 | int ipl=-1, igt=-1; | ^~~ bcfutils.c: In function ‘bcf_fix_gt’: bcfutils.c:254:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 254 | else | ^~~~ bcfutils.c:256:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 256 | b->fmt[0] = 'G'; b->fmt[1] = 'T'; b->fmt[2] = ':'; | ^ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o em.c: In function ‘bcf_em1’: em.c:174:12: warning: variable ‘n2’ set but not used [-Wunused-but-set-variable] 174 | int i, n, n2; | ^~ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o make[2]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/SICtools/src/bcftools' make[2]: Entering directory '/home/biocbuild/bbs-3.20-bioc/meat/SICtools/src/misc' make[2]: Nothing to be done for 'lib'. make[2]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/SICtools/src/misc' gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o bam_plcmd.c: In function ‘mpileup’: bam_plcmd.c:333:28: warning: variable ‘ref16’ set but not used [-Wunused-but-set-variable] 333 | int total_depth, _ref0, ref16; | ^~~~~ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o bam2bcf.c: In function ‘bcf_call2bcf’: bam2bcf.c:428:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 428 | if (bc->read_pos_bias != -1 ) | ^~ bam2bcf.c:430:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 430 | kputc('\0', &s); | ^~~~~ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o bam2bcf_indel.c: In function ‘bcf_call_add_rg’: bam2bcf_indel.c:32:4: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 32 | for (r = p; *r && *r != '\t' && *r != '\n'; ++r); lp = r - p; | ^~~ bam2bcf_indel.c:32:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 32 | for (r = p; *r && *r != '\t' && *r != '\n'; ++r); lp = r - p; | ^~ bam2bcf_indel.c:33:4: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 33 | for (r = q; *r && *r != '\t' && *r != '\n'; ++r); lq = r - q; | ^~~ bam2bcf_indel.c:33:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 33 | for (r = q; *r && *r != '\t' && *r != '\n'; ++r); lq = r - q; | ^~ bam2bcf_indel.c: In function ‘bcf_call_gap_prep’: bam2bcf_indel.c:121:28: warning: variable ‘query’ set but not used [-Wunused-but-set-variable] 121 | char *inscns = 0, *ref2, *query, **ref_sample; | ^~~~~ bam2bcf_indel.c:121:21: warning: variable ‘ref2’ set but not used [-Wunused-but-set-variable] 121 | char *inscns = 0, *ref2, *query, **ref_sample; | ^~~~ bam2bcf_indel.c:120:16: warning: variable ‘ref_type’ set but not used [-Wunused-but-set-variable] 120 | int N, l_run, ref_type; | ^~~~~~~~ bam2bcf_indel.c:119:82: warning: variable ‘score2’ set but not used [-Wunused-but-set-variable] 119 | int i, s, j, k, t, n_types, *types, max_rd_len, left, right, max_ins, *score1, *score2, max_ref2; | ^~~~~~ bam2bcf_indel.c:119:73: warning: variable ‘score1’ set but not used [-Wunused-but-set-variable] 119 | int i, s, j, k, t, n_types, *types, max_rd_len, left, right, max_ins, *score1, *score2, max_ref2; | ^~~~~~ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o errmod.c: In function ‘errmod_cal’: errmod.c:79:8: warning: self-comparison always evaluates to false [-Wtautological-compare] 79 | if (m > m) return -1; | ^ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o cut_target.c: In function ‘main_cut_target’: cut_target.c:137:36: warning: variable ‘lastpos’ set but not used [-Wunused-but-set-variable] 137 | int c, tid, pos, n, lasttid = -1, lastpos = -1, l, max_l; | ^~~~~~~ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o gcc -g -Wall -O2 -o samtools2SIC bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread make[1]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/SICtools/src' make[1]: Entering directory '/home/biocbuild/bbs-3.20-bioc/meat/SICtools/src/bcftools' gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o call1.c: In function ‘write_header’: call1.c:303:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 303 | if (!strstr(str.s, "##FORMAT=<ID=GL,")) | ^~ call1.c:305:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 305 | if (!strstr(str.s, "##FORMAT=<ID=DP,")) | ^~ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o gcc -g -Wall -O2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread make[1]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/SICtools/src/bcftools' make[1]: Entering directory '/home/biocbuild/bbs-3.20-bioc/meat/SICtools/src/misc' gcc -c -g -Wall -O2 -DMD5SUM_MAIN -o md5sum-lite.o md5.c md5.c: In function ‘MD5Final’: md5.c:155:26: warning: argument to ‘sizeof’ in ‘memset’ call is the same expression as the destination; did you mean to dereference it? [-Wsizeof-pointer-memaccess] 155 | memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */ | ^ gcc -g -Wall -O2 -o md5sum-lite md5sum-lite.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o md5.c: In function ‘MD5Final’: md5.c:155:26: warning: argument to ‘sizeof’ in ‘memset’ call is the same expression as the destination; did you mean to dereference it? [-Wsizeof-pointer-memaccess] 155 | memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */ | ^ gcc -g -Wall -O2 -c -I.. -o md5fa.o md5fa.c gcc -g -Wall -O2 -o md5fa md5.o md5fa.o -lz gcc -g -Wall -O2 -o maq2sam-short maq2sam.c -lz gcc -g -Wall -O2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz gcc -g -Wall -O2 -c -I.. -o ace2sam.o ace2sam.c ace2sam.c: In function ‘main’: ace2sam.c:162:4: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 162 | if (write_cns) puts(t[4].s); t[4].l = 0; | ^~ ace2sam.c:162:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 162 | if (write_cns) puts(t[4].s); t[4].l = 0; | ^ gcc -g -Wall -O2 -o ace2sam ace2sam.o -lz gcc -g -Wall -O2 -c -I.. -o wgsim.o wgsim.c gcc -g -Wall -O2 -o wgsim wgsim.o -lm -lz gcc -g -Wall -O2 -c -I.. -o bamcheck.o bamcheck.c gcc -g -Wall -O2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz make[1]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/SICtools/src/misc' installing via 'install.libs.R' to /home/biocbuild/R/R-4.4.1/site-library/00LOCK-SICtools/00new/SICtools ** R ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘plyr::count’ by ‘matrixStats::count’ when loading ‘SICtools’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import ‘plyr::count’ by ‘matrixStats::count’ when loading ‘SICtools’ ** testing if installed package can be loaded from final location Warning: replacing previous import ‘plyr::count’ by ‘matrixStats::count’ when loading ‘SICtools’ ** testing if installed package keeps a record of temporary installation path * DONE (SICtools)
SICtools.Rcheck/tests/runTests.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > ## runTests > > BiocGenerics:::testPackage("SICtools") Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Attaching package: 'plyr' The following object is masked from 'package:matrixStats': count The following object is masked from 'package:XVector': compact The following object is masked from 'package:IRanges': desc The following object is masked from 'package:S4Vectors': rename [1] "chr07" "828636" "G" [1] "chr07" "828714" "C" [1] "chr04 1 1531933" [1] "chr04 962501 1026983" RUNIT TEST PROTOCOL -- Sat Oct 19 09:52:45 2024 *********************************************** Number of test functions: 2 Number of errors: 0 Number of failures: 0 1 Test Suite : SICtools RUnit Tests - 2 test functions, 0 errors, 0 failures Number of test functions: 2 Number of errors: 0 Number of failures: 0 Warning messages: 1: replacing previous import 'plyr::count' by 'matrixStats::count' when loading 'SICtools' 2: In applyPileups(ppFiles, calcInfoRange, param = regSplitParam) : 'applyPileups' is deprecated. Use 'pileup' instead. See help("Deprecated") 3: In applyPileups(ppFiles, calcInfoRange, param = regSplitParam) : 'applyPileups' is deprecated. Use 'pileup' instead. See help("Deprecated") > > > > > proc.time() user system elapsed 18.918 0.594 19.457
SICtools.Rcheck/SICtools-Ex.timings
name | user | system | elapsed | |
indelDiff | 4.655 | 0.107 | 4.784 | |
snpDiff | 0.132 | 0.024 | 0.157 | |