Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
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 506/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DECIPHER 3.1.2 (landing page) Erik Wright
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the DECIPHER package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DECIPHER.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. |
Package: DECIPHER |
Version: 3.1.2 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DECIPHER.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings DECIPHER_3.1.2.tar.gz |
StartedAt: 2024-06-10 01:41:24 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 02:01:13 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 1189.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: DECIPHER.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DECIPHER.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings DECIPHER_3.1.2.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/DECIPHER.Rcheck' * using R version 4.4.0 RC (2024-04-16 r86468 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'DECIPHER/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'DECIPHER' version '3.1.2' * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'DECIPHER' can be installed ... OK * used C compiler: 'gcc.exe (GCC) 13.2.0' * checking installed package size ... NOTE installed size is 12.5Mb sub-directories of 1Mb or more: R 1.4Mb data 7.5Mb extdata 2.5Mb * 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 ... OK * 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 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 AlignSeqs: no visible binding for global variable 'deltaGrulesRNA' DesignSignatures: no visible binding for global variable 'deltaHrules' FindGenes: no visible binding for global variable 'deltaHrulesRNA' FindNonCoding: no visible binding for global variable 'deltaHrulesRNA' LearnNonCoding: no visible binding for global variable 'deltaHrulesRNA' PredictDBN: no visible binding for global variable 'deltaGrulesRNA' TreeLine: multiple local function definitions for '.minimize' with different formal arguments Undefined global functions or variables: deltaGrulesRNA deltaHrules deltaHrulesRNA * 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 contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... 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 compiled code ... NOTE Note: information on .o files for x64 is not available File 'F:/biocbuild/bbs-3.20-bioc/R/library/DECIPHER/libs/x64/DECIPHER.dll': Found '_assert', possibly from 'assert' (C) Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) 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 sizes of PDF files under 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed AlignSeqs 194.00 8.23 202.27 LearnNonCoding 106.75 7.56 114.36 MapCharacters 88.56 0.59 89.16 FindNonCoding 61.91 10.49 72.87 ExtractGenes 61.91 2.42 64.37 FindGenes 59.08 3.09 62.21 Genes-class 58.87 2.67 61.82 WriteGenes 58.01 2.52 60.52 DetectRepeats 35.88 2.39 38.28 BrowseSeqs 33.61 1.26 34.92 CorrectFrameshifts 18.87 1.22 20.09 StaggerAlignment 14.70 2.22 16.93 AlignTranslation 14.47 0.91 15.39 Taxa-class 11.10 0.50 11.59 TreeLine 10.29 0.47 10.77 IdTaxa 9.69 0.52 10.23 LearnTaxa 7.28 2.33 9.63 DesignArray 7.46 0.05 7.51 Array2Matrix 6.93 0.01 6.93 Clusterize 6.25 0.36 6.61 ScoreAlignment 5.06 0.51 5.58 * 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: 3 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/DECIPHER.Rcheck/00check.log' for details.
DECIPHER.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL DECIPHER ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'DECIPHER' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.2.0' gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c AlignProfiles.c -o AlignProfiles.o AlignProfiles.c: In function 'alignProfiles._omp_fn.0': AlignProfiles.c:437:37: warning: 'lGs' may be used uninitialized [-Wmaybe-uninitialized] 437 | lGs *= tot; | ~~~~^~~~~~ AlignProfiles.c:61:51: note: 'lGs' was declared here 61 | double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS, temp, avgM = 0; | ^~~ AlignProfiles.c:435:37: warning: 'lGp' may be used uninitialized [-Wmaybe-uninitialized] 435 | lGp *= tot; | ~~~~^~~~~~ AlignProfiles.c:61:46: note: 'lGp' was declared here 61 | double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS, temp, avgM = 0; | ^~~ AlignProfiles.c: In function 'alignProfilesAA._omp_fn.0': AlignProfiles.c:1290:37: warning: 'lGs' may be used uninitialized [-Wmaybe-uninitialized] 1290 | lGs *= tot; | ~~~~^~~~~~ AlignProfiles.c:819:51: note: 'lGs' was declared here 819 | double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R, temp, avgM = 0; | ^~~ AlignProfiles.c:1288:37: warning: 'lGp' may be used uninitialized [-Wmaybe-uninitialized] 1288 | lGp *= tot; | ~~~~^~~~~~ AlignProfiles.c:819:46: note: 'lGp' was declared here 819 | double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R, temp, avgM = 0; | ^~~ AlignProfiles.c: In function 'alignProfiles': AlignProfiles.c:388:25: warning: 'subM' may be used uninitialized [-Wmaybe-uninitialized] 388 | #pragma omp parallel for private(i,j,gp,gs,S,M,GP,GS,tot,lGp,lGs,temp) reduction(+:totM,avgM) num_threads(NTHREADS) | ^~~ AlignProfiles.c:81:17: note: 'subM' was declared here 81 | double *subM; | ^~~~ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c AssignIndels.c -o AssignIndels.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Biostrings_stubs.c -o Biostrings_stubs.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c CalculateDeltaG.c -o CalculateDeltaG.o CalculateDeltaG.c: In function 'calculateHairpinDeltaG': CalculateDeltaG.c:463:36: warning: 's1' may be used uninitialized [-Wmaybe-uninitialized] 463 | if ((!((s1 == 4) && (s2 == 4)) || j >= a[i]) && count > 3) { | ~~~~^~~~~ CalculateDeltaG.c:375:29: note: 's1' was declared here 375 | int i, j, k, count, s1, s2; | ^~ CalculateDeltaG.c:463:49: warning: 's2' may be used uninitialized [-Wmaybe-uninitialized] 463 | if ((!((s1 == 4) && (s2 == 4)) || j >= a[i]) && count > 3) { | ~~~~^~~~~ CalculateDeltaG.c:375:33: note: 's2' was declared here 375 | int i, j, k, count, s1, s2; | ^~ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c CalculateFISH.c -o CalculateFISH.o CalculateFISH.c: In function 'calculateFISH': CalculateFISH.c:25:30: warning: missing braces around initializer [-Wmissing-braces] 25 | double dH_DR[4][4] = { | ^ 26 | -11.5, -7.8, -7, -8.3, | { } 27 | -10.4, -12.8, -16.3, -9.1, | { } 28 | -8.6, -8, -9.3, -5.9, | { } 29 | -7.8, -5.5, -9, -7.8 | { 30 | }; | } CalculateFISH.c:31:30: warning: missing braces around initializer [-Wmissing-braces] 31 | double dS_DR[4][4] = { | ^ 32 | -36.4, -21.6, -19.7, -23.9, | { } 33 | -28.4, -31.9, -47.1, -23.5, | { } 34 | -22.9, -17.1, -23.2, -12.3, | { } 35 | -23.2, -13.5, -26.1, -21.9 | { 36 | }; | } CalculateFISH.c:37:30: warning: missing braces around initializer [-Wmissing-braces] 37 | double dH_DD[4][4] = { | ^ 38 | -7.9, -8.4, -7.8, -7.2, | { } 39 | -8.5, -8, -10.6, -7.8, | { } 40 | -8.2, -9.8, -8, -8.4, | { } 41 | -7.2, -8.2, -8.5, -7.9 | { 42 | }; | } CalculateFISH.c:43:30: warning: missing braces around initializer [-Wmissing-braces] 43 | double dS_DD[4][4] = { | ^ 44 | -22.2, -22.4, -21, -20.4, | { } 45 | -22.7, -19.9, -27.2, -21, | { } 46 | -22.2, -24.4, -19.9, -22.4, | { } 47 | -21.3, -22.2, -22.7, -22.2 | { 48 | }; | } CalculateFISH.c:49:30: warning: missing braces around initializer [-Wmissing-braces] 49 | double dH_RR[4][4] = { | ^ 50 | -6.6, -10.17, -7.65, -5.76, | { } 51 | -10.56, -12.21, -7.95, -7.65, | { } 52 | -13.37, -14.21, -12.21, -10.17, | { } 53 | -8.11, -13.37, -10.56, -6.6 | { 54 | }; | } CalculateFISH.c:55:30: warning: missing braces around initializer [-Wmissing-braces] 55 | double dS_RR[4][4] = { | ^ 56 | -18.38, -26.03, -19.18, -15.67, | { } 57 | -28.25, -30.02, -19.18, -19.18, | { } 58 | -35.68, -34.85, -30.02, -26.03, | { } 59 | -22.59, -35.68, -28.25, -18.38 | { 60 | }; | } gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ChainSegments.c -o ChainSegments.o ChainSegments.c: In function 'chainSegments': ChainSegments.c:524:49: warning: 'upY' may be used uninitialized [-Wmaybe-uninitialized] 524 | if (minX == minY && upX == upY) { | ~~~~^~~~~~ ChainSegments.c:490:93: note: 'upY' was declared here 490 | int minDx = 2e9, minDy = 2e9, minX = -1, minY = -2, merge = 0, upX, upY; | ^~~ ChainSegments.c:524:49: warning: 'upX' may be used uninitialized [-Wmaybe-uninitialized] 524 | if (minX == minY && upX == upY) { | ~~~~^~~~~~ ChainSegments.c:490:88: note: 'upX' was declared here 490 | int minDx = 2e9, minDy = 2e9, minX = -1, minY = -2, merge = 0, upX, upY; | ^~~ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Cluster.c -o Cluster.o Cluster.c: In function 'cluster._omp_fn.0': Cluster.c:418:50: warning: 'minC' may be used uninitialized [-Wmaybe-uninitialized] 418 | minCs[i] = minC; | ~~~~~~~~~^~~~~~ Cluster.c:246:57: note: 'minC' was declared here 246 | int k, dobj, clusterNum, minRow, minCol, index, minC, met; | ^~~~ Cluster.c: In function 'cluster._omp_fn.1': Cluster.c:442:72: warning: 'minC' may be used uninitialized [-Wmaybe-uninitialized] 442 | minCols[rowIndices[i]] = minC; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ Cluster.c:246:57: note: 'minC' was declared here 246 | int k, dobj, clusterNum, minRow, minCol, index, minC, met; | ^~~~ Cluster.c: In function 'cluster': Cluster.c:408:41: warning: 'nDiv' may be used uninitialized [-Wmaybe-uninitialized] 408 | #pragma omp parallel for private(i,j,minC,minH) schedule(guided) num_threads(nthreads) | ^~~ Cluster.c:283:17: note: 'nDiv' was declared here 283 | double *nDiv; | ^~~~ Cluster.c:392:72: warning: 'minC' may be used uninitialized [-Wmaybe-uninitialized] 392 | minCols[rowIndices[i]] = minC; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ Cluster.c:246:57: note: 'minC' was declared here 246 | int k, dobj, clusterNum, minRow, minCol, index, minC, met; | ^~~~ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClusterML.c -o ClusterML.o ClusterML.c: In function 'clusterML': ClusterML.c:1293:17: warning: 'node' may be used uninitialized [-Wmaybe-uninitialized] 1293 | #pragma omp parallel for private(j,k,o,p,y_i,row) num_threads(nthreads) | ^~~ ClusterML.c:1170:17: note: 'node' was declared here 1170 | double *node; | ^~~~ ClusterML.c:1293:17: warning: 'Up' may be used uninitialized [-Wmaybe-uninitialized] 1293 | #pragma omp parallel for private(j,k,o,p,y_i,row) num_threads(nthreads) | ^~~ ClusterML.c:1206:14: note: 'Up' was declared here 1206 | int *Up; | ^~ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClusterMP.c -o ClusterMP.o ClusterMP.c: In function 'clusterMP._omp_fn.0': ClusterMP.c:165:41: warning: 'P' may be used uninitialized [-Wmaybe-uninitialized] 165 | allStates(R, P, S, c, j, 0, k - 1, 0, k - 1, c, only); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ClusterMP.c:153:30: note: 'P' was declared here 153 | int *P; | ^ ClusterMP.c:98:22: warning: 'm' may be used uninitialized [-Wmaybe-uninitialized] 98 | int i, j, k, m, w; | ^ ClusterMP.c: In function 'clusterMP': ClusterMP.c:140:17: warning: 'Up' may be used uninitialized [-Wmaybe-uninitialized] 140 | #pragma omp parallel for private(i,j,k,m,w) num_threads(nthreads) | ^~~ ClusterMP.c:126:14: note: 'Up' was declared here 126 | int *Up; | ^~ ClusterMP.c:140:17: warning: 'lengths' may be used uninitialized [-Wmaybe-uninitialized] 140 | #pragma omp parallel for private(i,j,k,m,w) num_threads(nthreads) | ^~~ ClusterMP.c:111:17: note: 'lengths' was declared here 111 | double *lengths, *score; | ^~~~~~~ ClusterMP.c:140:17: warning: 'nodes' may be used uninitialized [-Wmaybe-uninitialized] 140 | #pragma omp parallel for private(i,j,k,m,w) num_threads(nthreads) | ^~~ ClusterMP.c:112:14: note: 'nodes' was declared here 112 | int *nodes, *subM; | ^~~~~ ClusterMP.c:140:17: warning: 'subM' may be used uninitialized [-Wmaybe-uninitialized] 140 | #pragma omp parallel for private(i,j,k,m,w) num_threads(nthreads) | ^~~ ClusterMP.c:112:22: note: 'subM' was declared here 112 | int *nodes, *subM; | ^~~~ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Compositions.c -o Compositions.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Compression.c -o Compression.o Compression.c: In function 'nbit._omp_fn.0': Compression.c:1241:71: warning: 'lastTriplet' may be used uninitialized [-Wmaybe-uninitialized] 1241 | if (threeBitEnd > threeBitBegin && (j - lastTriplet) > 20) { | ~~~^~~~~~~~~~~~~~ Compression.c:631:26: note: 'lastTriplet' was declared here 631 | int run, lastTriplet, lastCase; | ^~~~~~~~~~~ Compression.c:1011:62: warning: 'word' may be used uninitialized [-Wmaybe-uninitialized] 1011 | word = (word << 8) | (unsigned int)reorder(byte); | ~~~~~~^~~~~ Compression.c:544:37: note: 'word' was declared here 544 | unsigned int *dict, word, count, lastHit, currHit, lastPos = 0; | ^~~~ Compression.c:1012:54: warning: 'count' may be used uninitialized [-Wmaybe-uninitialized] 1012 | count++; | ~~~~~^~ Compression.c:544:43: note: 'count' was declared here 544 | unsigned int *dict, word, count, lastHit, currHit, lastPos = 0; | ^~~~~ Compression.c:545:41: warning: 'rev' may be used uninitialized [-Wmaybe-uninitialized] 545 | int lastTemp, currTemp, rev, len, len2, thresh = 1; | ^~~ Compression.c:1215:58: warning: 'lastHit' may be used uninitialized [-Wmaybe-uninitialized] 1215 | p[c++] = (unsigned char)lastHit; | ^~~~~~~~~~~~~~~~~~~~~~ Compression.c:544:50: note: 'lastHit' was declared here 544 | unsigned int *dict, word, count, lastHit, currHit, lastPos = 0; | ^~~~~~~ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ConsensusSequence.c -o ConsensusSequence.o In function 'runsAA', inlined from 'consensusProfileAA' at ConsensusSequence.c:1836:3: ConsensusSequence.c:454:50: warning: 'lastPos' may be used uninitialized [-Wmaybe-uninitialized] 454 | if (lastGap < (s - 2)) // ensure continuity before the run | ~~~^~~~ ConsensusSequence.c: In function 'consensusProfileAA': ConsensusSequence.c:397:30: note: 'lastPos' was declared here 397 | int j, temp, length, lastPos, s = -1, value = -1, lastGap = start - 1; | ^~~~~~~ ConsensusSequence.c: In function 'colScores': ConsensusSequence.c:2043:19: warning: 'curr' may be used uninitialized [-Wmaybe-uninitialized] 2043 | if (tGaps && curr > 0) { | ~~~~~~^~~~~~~~~~~ ConsensusSequence.c:1930:37: note: 'curr' was declared here 1930 | double weight, total, prev, curr; | ^~~~ ConsensusSequence.c: In function 'colScoresAA': ConsensusSequence.c:2186:19: warning: 'curr' may be used uninitialized [-Wmaybe-uninitialized] 2186 | if (tGaps && curr > 0) { | ~~~~~~^~~~~~~~~~~ ConsensusSequence.c:2073:37: note: 'curr' was declared here 2073 | double weight, total, prev, curr; | ^~~~ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c DesignProbes.c -o DesignProbes.o DesignProbes.c: In function 'designProbes': DesignProbes.c:70:27: warning: missing braces around initializer [-Wmissing-braces] 70 | double NN[4][4] = { | ^ 71 | -0.816507461,-2.5401714,-1.647430026,-1.184658548 | { 72 | ,-1.854740485,-2.479102613,-2.826248182,-1.647430026 | }{ 73 | ,-2.48761723,-4.694133177,-2.479102613,-2.5401714 | }{ 74 | ,-0.495794417,-2.48761723,-1.854740485,-0.816507461 | }{ 75 | }; | } DesignProbes.c:77:27: warning: missing braces around initializer [-Wmissing-braces] 77 | double PM[4][4] = { | ^ 78 | -0.141370102,-0.439805276,-0.285236035,-0.205111781 | { 79 | ,-0.321129768,-0.429231826,-0.48933661,-0.285236035 | }{ 80 | ,-0.430706047,-0.812742218,-0.429231826,-0.439805276 | }{ 81 | ,-0.085841845,-0.430706047,-0.321129768,-0.141370102 | }{ 82 | }; | } DesignProbes.c:84:34: warning: missing braces around initializer [-Wmissing-braces] 84 | double sMM[4][5][5][4] = { | ^ 85 | 0,0,0,0 | {{{ 86 | ,1.545032445,1.254355018,1.491691514,1.329138183 | }{ 87 | ,1.150635633,0.582415494,1.075877275,1.187937642 | }{ 88 | ,1.203555051,1.001540513,0.864287715,0.717125848 | }{ 89 | ,0.75,0.65,0.69,0.78 | }{ 90 | ,0.630005348,0.18553379,0.730763505,0.709272397 | - | }},{{ 91 | ,0,0,0,0 | }{ 92 | ,0.856582783,-0.143236405,0.716721488,0.603652831 | }{ 93 | ,0.851622883,0.653168672,0.676545316,1.187937642 | }{ 94 | ,0.75,0.65,0.69,0.78 | }{ 95 | ,1.231861002,0.746214538,1.087821916,0.989140748 | - | }},{{ 96 | ,1.822113278,1.270687029,1.336192565,1.364584949 | }{ 97 | ,0,0,0,0 | }{ 98 | ,1.443665704,1.385046493,1.256013166,1.329138183 | }{ 99 | ,0.75,0.65,0.69,0.78 | }{ 100 | ,1.478009492,0.882097231,1.20450984,1.061002478 | - | }},{{ 101 | ,1.496720812,0.846496194,0.967868114,0.989140748 | }{ 102 | ,0.766581547,-0.024857805,0.50754303,0.709272397 | }{ 103 | ,0,0,0,0 | }{ 104 | ,0.75,0.65,0.69,0.78 | }{ 105 | ,0.75,0.65,0.69,0.78 | - | }},{{ 106 | ,0.75,0.65,0.69,0.78 | }{ 107 | ,0.75,0.65,0.69,0.78 | }{ 108 | ,0.76,0.65,0.69,0.78 | }{ 109 | ,0,0,0,0 | }{ 110 | ,0,0,0,0 | - | }}},{{{ 111 | ,1.295827995,0.84547091,0.91019099,1.256013166 | }{ 112 | ,0.755889609,0.241428373,0.396379912,0.676545316 | }{ 113 | ,0.99945386,0.740323132,0.435659206,0.864287715 | }{ 114 | ,0.65,0.55,0.48,0.69 | }{ 115 | ,0.843147406,0.101248351,0.49063599,0.50754303 | - | }},{{ 116 | ,0,0,0,0 | }{ 117 | ,1.0651638,0.249934344,0.699352949,0.716721488 | }{ 118 | ,0.871921533,0.59458138,0.396379912,1.075877275 | }{ 119 | ,0.65,0.56,0.49,0.69 | }{ 120 | ,1.07531714,0.318907854,0.653287717,0.967868114 | - | }},{{ 121 | ,1.099899195,0.730184613,0.661798984,1.336192565 | }{ 122 | ,0,0,0,0 | }{ 123 | ,1.45897431,1.318532145,0.91019099,1.491691514 | }{ 124 | ,0.65,0.56,0.49,0.69 | }{ 125 | ,1.242135174,0.894838095,1.108555445,1.20450984 | - | }},{{ 126 | ,0.911428974,0.524430101,0.653287717,1.087821916 | }{ 127 | ,0.503209827,0.274849491,0.49063599,0.730763505 | }{ 128 | ,0,0,0,0 | }{ 129 | ,0.65,0.55,0.48,0.69 | }{ 130 | ,0.65,0.55,0.48,0.69 | - | }},{{ 131 | ,0.65,0.56,0.49,0.69 | }{ 132 | ,0.65,0.56,0.49,0.69 | }{ 133 | ,0.65,0.55,0.48,0.69 | }{ 134 | ,0,0,0,0 | }{ 135 | ,0,0,0,0 | - | }}},{{{ 136 | ,1.100661785,0.969784756,1.318532145,1.385046493 | }{ 137 | ,0.565895968,-0.060347902,0.59458138,0.653168672 | }{ 138 | ,0.782168488,0.788161238,0.740323132,1.001540513 | }{ 139 | ,0.68,0.46,0.55,0.65 | }{ 140 | ,0.468913405,-0.469855984,0.274849491,-0.024857805 | - | }},{{ 141 | ,0,0,0,0 | }{ 142 | ,0.258195131,-0.70438632,0.249934344,-0.143236405 | }{ 143 | ,0.502914193,-0.060347902,0.241428373,0.582415494 | }{ 144 | ,0.68,0.47,0.56,0.65 | }{ 145 | ,0.584083861,0.258975454,0.524430101,0.846496194 | - | }},{{ 146 | ,0.968040559,0.797499702,0.730184613,1.270687029 | }{ 147 | ,0,0,0,0 | }{ 148 | ,1.081040749,0.969784756,0.84547091,1.254355018 | }{ 149 | ,0.68,0.47,0.56,0.65 | }{ 150 | ,1.048553951,0.728354541,0.894838095,0.882097231 | - | }},{{ 151 | ,0.88611252,0.258975454,0.318907854,0.746214538 | }{ 152 | ,0.239520858,-0.469855984,0.101248351,0.18553379 | }{ 153 | ,0,0,0,0 | }{ 154 | ,0.68,0.46,0.55,0.65 | }{ 155 | ,0.68,0.46,0.55,0.65 | - | }},{{ 156 | ,0.68,0.47,0.56,0.65 | }{ 157 | ,0.68,0.47,0.56,0.65 | }{ 158 | ,0.68,0.46,0.55,0.65 | }{ 159 | ,0,0,0,0 | }{ 160 | ,0,0,0,0 | - | }}},{{{ 161 | ,1.566899704,1.081040749,1.45897431,1.443665704 | }{ 162 | ,0.976725675,0.502914193,0.871921533,0.851622883 | }{ 163 | ,1.482046826,0.782168488,0.99945386,1.203555051 | }{ 164 | ,0.85,0.68,0.65,0.76 | }{ 165 | ,0.798628781,0.239520858,0.503209827,0.766581547 | - | }},{{ 166 | ,0,0,0,0 | }{ 167 | ,1.141098246,0.258195131,1.0651638,0.856582783 | }{ 168 | ,0.976725675,0.565895968,0.755889609,1.150635633 | }{ 169 | ,0.85,0.68,0.65,0.75 | }{ 170 | ,1.125403302,0.88611252,0.911428974,1.496720812 | - | }},{{ 171 | ,1.68169282,0.968040559,1.099899195,1.822113278 | }{ 172 | ,0,0,0,0 | }{ 173 | ,1.566899704,1.100661785,1.295827995,1.545032445 | }{ 174 | ,0.85,0.68,0.65,0.75 | }{ 175 | ,1.35948517,1.048553951,1.242135174,1.478009492 | - | }},{{ 176 | ,1.125403302,0.584083861,1.07531714,1.231861002 | }{ 177 | ,0.798628781,0.468913405,0.843147406,0.630005348 | }{ 178 | ,0,0,0,0 | }{ 179 | ,0.85,0.68,0.65,0.75 | }{ 180 | ,0.85,0.68,0.65,0.75 | - | }},{{ 181 | ,0.85,0.68,0.65,0.75 | }{ 182 | ,0.85,0.68,0.65,0.75 | }{ 183 | ,0.85,0.68,0.65,0.75 | }{ 184 | ,0,0,0,0 | }{ 185 | }; | }}} DesignProbes.c: In function 'designProbes._omp_fn.0': DesignProbes.c:837:60: warning: 'lastCycle' may be used uninitialized [-Wmaybe-uninitialized] 837 | if (thisCycle < lastCycle) { | ^ DesignProbes.c:269:58: note: 'lastCycle' was declared here 269 | int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles; | ^~~~~~~~~ DesignProbes.c:837:60: warning: 'thisCycle' may be used uninitialized [-Wmaybe-uninitialized] 837 | if (thisCycle < lastCycle) { | ^ DesignProbes.c:269:69: note: 'thisCycle' was declared here 269 | int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles; | ^~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Diff.c -o Diff.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c DistanceMatrix.c -o DistanceMatrix.o DistanceMatrix.c: In function 'firstSeqsPosEqual': DistanceMatrix.c:796:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 796 | if (!ci) | ^~ DistanceMatrix.c:799:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 799 | while (i < ex) { | ^~~~~ DistanceMatrix.c:818:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 818 | if (!cj) | ^~ DistanceMatrix.c:821:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 821 | while (j < ey) { | ^~~~~ DistanceMatrix.c: In function 'computeOverlap._omp_fn.0': DistanceMatrix.c:1374:66: warning: 'OV' may be used uninitialized [-Wmaybe-uninitialized] 1374 | (w1 <= w2 && (double)(OV + off)/(double)w2 < coverage)))) { | ~~~~^~~~~~ DistanceMatrix.c:883:92: note: 'OV' was declared here 883 | int i, j, k, l, n, p, d, lx, new, *t, *keep, *I, *X, *OX, pos, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, useMax; | ^~ DistanceMatrix.c:1374:66: warning: 'off' may be used uninitialized [-Wmaybe-uninitialized] 1374 | (w1 <= w2 && (double)(OV + off)/(double)w2 < coverage)))) { | ~~~~^~~~~~ DistanceMatrix.c:883:96: note: 'off' was declared here 883 | int i, j, k, l, n, p, d, lx, new, *t, *keep, *I, *X, *OX, pos, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, useMax; | ^~~ DistanceMatrix.c:1053:53: warning: 'one' may be used uninitialized [-Wmaybe-uninitialized] 1053 | two != one) { | ~~~~^~~~~~ DistanceMatrix.c:1028:29: note: 'one' was declared here 1028 | int one, two; | ^~~ DistanceMatrix.c:1390:52: warning: 'o' may be used uninitialized [-Wmaybe-uninitialized] 1390 | if (o == 1) { | ^ DistanceMatrix.c:883:112: note: 'o' was declared here 883 | int i, j, k, l, n, p, d, lx, new, *t, *keep, *I, *X, *OX, pos, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, useMax; | ^ DistanceMatrix.c:1393:91: warning: 'ov' may be used uninitialized [-Wmaybe-uninitialized] 1393 | sim[i] = (double)pos/((double)(ov + count + g2)); | ~~~^~~~~~~ DistanceMatrix.c:883:88: note: 'ov' was declared here 883 | int i, j, k, l, n, p, d, lx, new, *t, *keep, *I, *X, *OX, pos, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, useMax; | ^~ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c EnumerateSequence.c -o EnumerateSequence.o EnumerateSequence.c: In function 'pop': EnumerateSequence.c:545:15: warning: suggest parentheses around '+' in operand of '&' [-Wparentheses] 545 | x = x + (x >> 4) & 0xF0F0F0F; | ~~^~~~~~~~~~ EnumerateSequence.c: In function 'enumerateSequence': EnumerateSequence.c:358:17: warning: 'mN' may be used uninitialized [-Wmaybe-uninitialized] 358 | #pragma omp parallel for private(i,j,k,x_i,rans,sum,ambiguous) num_threads(nthreads) | ^~~ EnumerateSequence.c:317:14: note: 'mN' was declared here 317 | int *mN; | ^~ EnumerateSequence.c:358:17: warning: 'tot' may be used uninitialized [-Wmaybe-uninitialized] 358 | #pragma omp parallel for private(i,j,k,x_i,rans,sum,ambiguous) num_threads(nthreads) | ^~~ EnumerateSequence.c:318:13: note: 'tot' was declared here 318 | int tot; // total number of k-mers | ^~~ EnumerateSequence.c: In function 'enumerateSequenceReducedAA': EnumerateSequence.c:955:17: warning: 'mN' may be used uninitialized [-Wmaybe-uninitialized] 955 | #pragma omp parallel for private(i,j,k,x_i,rans,sum,ambiguous) num_threads(nthreads) | ^~~ EnumerateSequence.c:907:14: note: 'mN' was declared here 907 | int *mN; | ^~ EnumerateSequence.c:955:17: warning: 'tot' may be used uninitialized [-Wmaybe-uninitialized] 955 | #pragma omp parallel for private(i,j,k,x_i,rans,sum,ambiguous) num_threads(nthreads) | ^~~ EnumerateSequence.c:908:13: note: 'tot' was declared here 908 | int tot; // total number of k-mers | ^~~ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ExpandAmbiguities.c -o ExpandAmbiguities.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FindFrameshifts.c -o FindFrameshifts.o FindFrameshifts.c: In function 'findFrameshifts': FindFrameshifts.c:464:43: warning: 'rPercentComplete' may be used uninitialized [-Wmaybe-uninitialized] 464 | *rPercentComplete = floor(100*(double)(s + 1)/f_length); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FindFrameshifts.c:160:25: note: 'rPercentComplete' was declared here 160 | int before, v, *rPercentComplete; | ^~~~~~~~~~~~~~~~ In file included from F:/biocbuild/bbs-3.20-bioc/R/include/Rdefines.h:41, from FindFrameshifts.c:11: F:/biocbuild/bbs-3.20-bioc/R/include/Rinternals.h:901:33: warning: 'percentComplete' may be used uninitialized [-Wmaybe-uninitialized] 901 | #define eval Rf_eval FindFrameshifts.c:467:33: note: in expansion of macro 'eval' 467 | eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage); | ^~~~ FindFrameshifts.c:162:14: note: 'percentComplete' was declared here 162 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~~~~ F:/biocbuild/bbs-3.20-bioc/R/include/Rinternals.h:901:33: warning: 'utilsPackage' may be used uninitialized [-Wmaybe-uninitialized] 901 | #define eval Rf_eval FindFrameshifts.c:467:33: note: in expansion of macro 'eval' 467 | eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage); | ^~~~ FindFrameshifts.c:162:31: note: 'utilsPackage' was declared here 162 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~ FindFrameshifts.c:317:34: warning: 'I' may be used uninitialized [-Wmaybe-uninitialized] 317 | while (i > 0 && j > 0) { | ~~^~~ FindFrameshifts.c:135:28: note: 'I' was declared here 135 | int s, o, i, j, k, I, J, K, n, m, w, r, c, rc; | ^ FindFrameshifts.c:317:43: warning: 'J' may be used uninitialized [-Wmaybe-uninitialized] 317 | while (i > 0 && j > 0) { | ~~^~~ FindFrameshifts.c:135:31: note: 'J' was declared here 135 | int s, o, i, j, k, I, J, K, n, m, w, r, c, rc; | ^ FindFrameshifts.c:376:28: warning: 'K' may be used uninitialized [-Wmaybe-uninitialized] 376 | if (k == 1) { | ^ FindFrameshifts.c:135:34: note: 'K' was declared here 135 | int s, o, i, j, k, I, J, K, n, m, w, r, c, rc; | ^ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c GeneFinding.c -o GeneFinding.o GeneFinding.c: In function 'scoreCodonModel': GeneFinding.c:421:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 421 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:388:22: note: 'x_i.ptr' was declared here 388 | Chars_holder x_i; | ^~~ GeneFinding.c:431:57: warning: 'lastVal' may be used uninitialized [-Wmaybe-uninitialized] 431 | if (val < 64 && lastVal < 64) | ~~~~~~~~^~~~ GeneFinding.c:371:32: note: 'lastVal' was declared here 371 | int i, j, s, fin, val, lastVal, dicodon; | ^~~~~~~ GeneFinding.c: In function 'startCodonModel': GeneFinding.c:795:46: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 795 | val = getBase(x_i.ptr[j--]); | ^ GeneFinding.c:771:22: note: 'x_i.ptr' was declared here 771 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'scoreStartCodonModel': GeneFinding.c:896:46: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 896 | val = getBase(x_i.ptr[j--]); | ^ GeneFinding.c:868:22: note: 'x_i.ptr' was declared here 868 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'initialCodonModel': GeneFinding.c:951:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 951 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:928:22: note: 'x_i.ptr' was declared here 928 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'scoreInitialCodonModel': GeneFinding.c:1058:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 1058 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1031:22: note: 'x_i.ptr' was declared here 1031 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'terminationCodonModel': GeneFinding.c:1115:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 1115 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1092:22: note: 'x_i.ptr' was declared here 1092 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'scoreTerminationCodonModel': GeneFinding.c:1215:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 1215 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1188:22: note: 'x_i.ptr' was declared here 1188 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'getRegion': GeneFinding.c:1316:81: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 1316 | seq[k] = getBaseLetterRC(x_i.ptr[j--]); | ^ GeneFinding.c:1252:22: note: 'x_i.ptr' was declared here 1252 | Chars_holder x_i; | ^~~ GeneFinding.c:1313:51: warning: 'x_i.length' may be used uninitialized [-Wmaybe-uninitialized] 1313 | (s == 0 && j >= 0 && j + w <= x_i.length)) { | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ GeneFinding.c:1252:22: note: 'x_i.length' was declared here 1252 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'autocorrelationModel': GeneFinding.c:1378:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 1378 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1350:22: note: 'x_i.ptr' was declared here 1350 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'scoreAutocorrelationModel': GeneFinding.c:1495:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 1495 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1461:22: note: 'x_i.ptr' was declared here 1461 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'couplingModel': GeneFinding.c:1597:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 1597 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1573:22: note: 'x_i.ptr' was declared here 1573 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'scoreCouplingModel': GeneFinding.c:1711:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 1711 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1681:22: note: 'x_i.ptr' was declared here 1681 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'nucleotideBiasModel': GeneFinding.c:1826:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 1826 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1788:22: note: 'x_i.ptr' was declared here 1788 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'scoreNucleotideBiasModel': GeneFinding.c:1913:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 1913 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1882:22: note: 'x_i.ptr' was declared here 1882 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'upstreamMotifModel': GeneFinding.c:1992:75: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 1992 | val += mult[k - 1]*getBase(x_i.ptr[j - k + 1]); | ^ GeneFinding.c:1950:22: note: 'x_i.ptr' was declared here 1950 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'scoreUpstreamMotifModel': GeneFinding.c:2092:75: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 2092 | val += mult[k - 1]*getBase(x_i.ptr[j - k + 1]); | ^ GeneFinding.c:2057:22: note: 'x_i.ptr' was declared here 2057 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'scoreRunLengthModel': GeneFinding.c:2307:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 2307 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:2276:22: note: 'x_i.ptr' was declared here 2276 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'stopCodonModel': GeneFinding.c:2423:46: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 2423 | val = getBase(x_i.ptr[j--]); | ^ GeneFinding.c:2399:22: note: 'x_i.ptr' was declared here 2399 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'scoreStopCodonModel': GeneFinding.c:2524:46: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 2524 | val = getBase(x_i.ptr[j--]); | ^ GeneFinding.c:2496:22: note: 'x_i.ptr' was declared here 2496 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'codonFrequencies': GeneFinding.c:2577:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 2577 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:2554:22: note: 'x_i.ptr' was declared here 2554 | Chars_holder x_i; | ^~~ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c GetPools.c -o GetPools.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Import.c -o Import.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c InformationContent.c -o InformationContent.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c IntDist.c -o IntDist.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ManipulateXStringSet.c -o ManipulateXStringSet.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c MeltPolymer.c -o MeltPolymer.o MeltPolymer.c: In function 'meltPolymer': MeltPolymer.c:79:27: warning: missing braces around initializer [-Wmissing-braces] 79 | double dH[4][4] = { | ^ 80 | -7.9,-8.4,-7.8,-7.2 | { 81 | ,-8.5,-8.0,-10.6,-7.8 | }{ 82 | ,-8.2,-9.8,-8.0,-8.4 | }{ 83 | ,-7.2,-8.2,-8.5,-7.9 | }{ 84 | }; | } MeltPolymer.c:88:27: warning: missing braces around initializer [-Wmissing-braces] 88 | double dS[4][4] = { | ^ 89 | -22.2,-22.4,-21.0,-20.4 | { 90 | ,-22.7,-19.9,-27.2,-21.0 | }{ 91 | ,-22.2,-24.4,-19.9,-22.4 | }{ 92 | ,-21.3,-22.2,-22.7,-22.2 | }{ 93 | }; | } MeltPolymer.c:406:25: warning: 'ans' may be used uninitialized [-Wmaybe-uninitialized] 406 | SET_VECTOR_ELT(ret, s, ans); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ MeltPolymer.c:53:19: note: 'ans' was declared here 53 | SEXP ret, ans; | ^~~ MeltPolymer.c:358:41: warning: 'rans' may be used uninitialized [-Wmaybe-uninitialized] 358 | *(rans + k + l*s) += 1; | ^~~~~~~~~~~~~~~~~ MeltPolymer.c:54:17: note: 'rans' was declared here 54 | double *rans; | ^~~~ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c MovingAverage.c -o MovingAverage.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c NNLS.c -o NNLS.o NNLS.c: In function 'NNLS': NNLS.c:77:51: warning: 'rPercentComplete' may be used uninitialized [-Wmaybe-uninitialized] 77 | *rPercentComplete = floor(100*((double)i + 1)/(double)l); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NNLS.c:39:34: note: 'rPercentComplete' was declared here 39 | int i, j, k, before, v, *rPercentComplete; | ^~~~~~~~~~~~~~~~ In file included from F:/biocbuild/bbs-3.20-bioc/R/include/Rdefines.h:41, from NNLS.c:16: F:/biocbuild/bbs-3.20-bioc/R/include/Rinternals.h:901:33: warning: 'percentComplete' may be used uninitialized [-Wmaybe-uninitialized] 901 | #define eval Rf_eval NNLS.c:81:41: note: in expansion of macro 'eval' 81 | eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage); | ^~~~ NNLS.c:47:14: note: 'percentComplete' was declared here 47 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~~~~ F:/biocbuild/bbs-3.20-bioc/R/include/Rinternals.h:901:33: warning: 'utilsPackage' may be used uninitialized [-Wmaybe-uninitialized] 901 | #define eval Rf_eval NNLS.c:81:41: note: in expansion of macro 'eval' 81 | eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage); | ^~~~ NNLS.c:47:31: note: 'utilsPackage' was declared here 47 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Order.c -o Order.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PairwiseAlignment.c -o PairwiseAlignment.o PairwiseAlignment.c: In function 'alignPair._omp_fn.0': PairwiseAlignment.c:445:39: warning: 'p3' may be used uninitialized [-Wmaybe-uninitialized] 445 | p3[0] = l1; | ~~~~~~^~~~ PairwiseAlignment.c:175:24: note: 'p3' was declared here 175 | int *p1, *p2, *p3, *p4; | ^~ PairwiseAlignment.c:446:39: warning: 'p4' may be used uninitialized [-Wmaybe-uninitialized] 446 | p4[0] = l2 - j1; | ~~~~~~^~~~~~~~~ PairwiseAlignment.c:175:29: note: 'p4' was declared here 175 | int *p1, *p2, *p3, *p4; | ^~ PairwiseAlignment.c:449:39: warning: 'p1' may be used uninitialized [-Wmaybe-uninitialized] 449 | p1[0] = l2; | ~~~~~~^~~~ PairwiseAlignment.c:175:14: note: 'p1' was declared here 175 | int *p1, *p2, *p3, *p4; | ^~ PairwiseAlignment.c:450:39: warning: 'p2' may be used uninitialized [-Wmaybe-uninitialized] 450 | p2[0] = l1 - i1; | ~~~~~~^~~~~~~~~ PairwiseAlignment.c:175:19: note: 'p2' was declared here 175 | int *p1, *p2, *p3, *p4; | ^~ PairwiseAlignment.c: In function 'alignPairs': PairwiseAlignment.c:1107:17: warning: 'rPercentComplete' may be used uninitialized [-Wmaybe-uninitialized] 1107 | #pragma omp parallel for private(i) schedule(dynamic) num_threads(nthreads) | ^~~ PairwiseAlignment.c:1035:25: note: 'rPercentComplete' was declared here 1035 | int before, v, *rPercentComplete; | ^~~~~~~~~~~~~~~~ PairwiseAlignment.c:1107:17: warning: 'percentComplete' may be used uninitialized [-Wmaybe-uninitialized] 1107 | #pragma omp parallel for private(i) schedule(dynamic) num_threads(nthreads) | ^~~ PairwiseAlignment.c:1037:14: note: 'percentComplete' was declared here 1037 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~~~~ PairwiseAlignment.c:1107:17: warning: 'utilsPackage' may be used uninitialized [-Wmaybe-uninitialized] 1107 | #pragma omp parallel for private(i) schedule(dynamic) num_threads(nthreads) | ^~~ PairwiseAlignment.c:1037:31: note: 'utilsPackage' was declared here 1037 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PredictDBN.c -o PredictDBN.o PredictDBN.c: In function 'predictDBN': PredictDBN.c:597:25: warning: 'leftSymbol' may be used uninitialized [-Wmaybe-uninitialized] 597 | Traceback(MI, tot, unpaired, pos, states, leftSymbol, rightSymbol, 0, l - 1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PredictDBN.c:485:14: note: 'leftSymbol' was declared here 485 | char leftSymbol, rightSymbol; | ^~~~~~~~~~ PredictDBN.c:597:25: warning: 'rightSymbol' may be used uninitialized [-Wmaybe-uninitialized] 597 | Traceback(MI, tot, unpaired, pos, states, leftSymbol, rightSymbol, 0, l - 1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PredictDBN.c:485:26: note: 'rightSymbol' was declared here 485 | char leftSymbol, rightSymbol; | ^~~~~~~~~~~ In file included from F:/biocbuild/bbs-3.20-bioc/R/include/Rdefines.h:38, from PredictDBN.c:16: F:/biocbuild/bbs-3.20-bioc/R/include/R_ext/RS.h:55:25: warning: 'MI' may be used uninitialized [-Wmaybe-uninitialized] 55 | #define Free(p) (R_chk_free( (void *)(p) ), (p) = NULL) | ^~~~~~~~~~~~~~~~~~~~~~~~~ PredictDBN.c:1071:9: note: in expansion of macro 'Free' 1071 | Free(MI); | ^~~~ PredictDBN.c:236:17: note: 'MI' was declared here 236 | double *MI = Calloc(tot*tot, double); // initialized to zero | ^~ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PredictHEC.c -o PredictHEC.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_init_decipher.c -o R_init_decipher.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Search.c -o Search.o Search.c: In function 'searchIndex._omp_fn.0': Search.c:475:75: warning: 'maxLen' may be used uninitialized [-Wmaybe-uninitialized] 475 | if (deltaTarget >= maxSep + maxLen) { | ~~~~~~~^~~~~~~~ Search.c:449:37: note: 'maxLen' was declared here 449 | int maxLen; // maximum observed length | ^~~~~~ Search.c:443:51: warning: 's_j.ptr' may be used uninitialized [-Wmaybe-uninitialized] 443 | Chars_holder p_i, s_j; | ^~~ Search.c: In function 'searchIndex': Search.c:208:17: warning: 'sM' may be used uninitialized [-Wmaybe-uninitialized] 208 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:104:17: note: 'sM' was declared here 104 | double *sM, dS; | ^~ Search.c:208:17: warning: 'dS' may be used uninitialized [-Wmaybe-uninitialized] 208 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:104:21: note: 'dS' was declared here 104 | double *sM, dS; | ^~ Search.c:208:17: warning: 'lkup_row' may be used uninitialized [-Wmaybe-uninitialized] 208 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:105:14: note: 'lkup_row' was declared here 105 | int *lkup_row, *lkup_col; | ^~~~~~~~ Search.c:208:17: warning: 'lkup_col' may be used uninitialized [-Wmaybe-uninitialized] 208 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:105:25: note: 'lkup_col' was declared here 105 | int *lkup_row, *lkup_col; | ^~~~~~~~ Search.c:208:17: warning: 'rPercentComplete' may be used uninitialized [-Wmaybe-uninitialized] 208 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:133:25: note: 'rPercentComplete' was declared here 133 | int before, v, *rPercentComplete; | ^~~~~~~~~~~~~~~~ Search.c:208:17: warning: 'percentComplete' may be used uninitialized [-Wmaybe-uninitialized] 208 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:135:14: note: 'percentComplete' was declared here 135 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~~~~ Search.c:208:17: warning: 'utilsPackage' may be used uninitialized [-Wmaybe-uninitialized] 208 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:135:31: note: 'utilsPackage' was declared here 135 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~ Search.c:208:17: warning: 'matrices' may be used uninitialized [-Wmaybe-uninitialized] 208 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:201:16: note: 'matrices' was declared here 201 | int ***matrices; | ^~~~~~~~ Search.c:943:38: warning: 'anchors' may be used uninitialized [-Wmaybe-uninitialized] 943 | int *anchor = anchors[j]; | ^~~~~~ Search.c:888:15: note: 'anchors' was declared here 888 | int **anchors; // pointers to anchor positions | ^~~~~~~ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c TerminalMismatch.c -o TerminalMismatch.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Translate.c -o Translate.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Utils.c -o Utils.o Utils.c: In function 'splitPartitions': Utils.c:982:35: warning: 'change' may be used uninitialized [-Wmaybe-uninitialized] 982 | } else if (change - j >= m && // large enough partition | ~~~~~~~^~~ Utils.c:976:13: note: 'change' was declared here 976 | int change; // index before start of partition | ^~~~~~ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c VectorSums.c -o VectorSums.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c XVector_stubs.c -o XVector_stubs.o gcc -shared -s -static-libgcc -o DECIPHER.dll tmp.def AlignProfiles.o AssignIndels.o Biostrings_stubs.o CalculateDeltaG.o CalculateFISH.o ChainSegments.o Cluster.o ClusterML.o ClusterMP.o Compositions.o Compression.o ConsensusSequence.o DesignProbes.o Diff.o DistanceMatrix.o EnumerateSequence.o ExpandAmbiguities.o FindFrameshifts.o GeneFinding.o GetPools.o Import.o InformationContent.o IntDist.o ManipulateXStringSet.o MeltPolymer.o MovingAverage.o NNLS.o Order.o PairwiseAlignment.o PredictDBN.o PredictHEC.o R_init_decipher.o S4Vectors_stubs.o Search.o TerminalMismatch.o Translate.o Utils.o VectorSums.o XVector_stubs.o -fopenmp -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-DECIPHER/00new/DECIPHER/libs/x64 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (DECIPHER)
DECIPHER.Rcheck/DECIPHER-Ex.timings
name | user | system | elapsed | |
AA_REDUCED | 0.03 | 0.03 | 0.07 | |
Add2DB | 0.85 | 0.33 | 1.21 | |
AdjustAlignment | 0.30 | 0.01 | 0.31 | |
AlignDB | 1.64 | 0.04 | 1.69 | |
AlignPairs | 3.75 | 0.03 | 3.78 | |
AlignProfiles | 1.22 | 0.10 | 1.31 | |
AlignSeqs | 194.00 | 8.23 | 202.27 | |
AlignSynteny | 3.11 | 0.06 | 3.18 | |
AlignTranslation | 14.47 | 0.91 | 15.39 | |
AmplifyDNA | 0.01 | 0.02 | 0.04 | |
Array2Matrix | 6.93 | 0.01 | 6.93 | |
BLOSUM | 0.01 | 0.02 | 0.03 | |
BrowseDB | 0.06 | 0.03 | 0.10 | |
BrowseSeqs | 33.61 | 1.26 | 34.92 | |
CalculateEfficiencyArray | 0.03 | 0.00 | 0.03 | |
CalculateEfficiencyFISH | 0 | 0 | 0 | |
CalculateEfficiencyPCR | 0.02 | 0.00 | 0.02 | |
Clusterize | 6.25 | 0.36 | 6.61 | |
Codec | 1.23 | 0.02 | 1.26 | |
ConsensusSequence | 0.18 | 0.01 | 0.19 | |
Cophenetic | 0.20 | 0.02 | 0.22 | |
CorrectFrameshifts | 18.87 | 1.22 | 20.09 | |
CreateChimeras | 0.8 | 0.0 | 0.8 | |
DB2Seqs | 0.05 | 0.01 | 0.06 | |
DesignArray | 7.46 | 0.05 | 7.51 | |
DesignPrimers | 0.01 | 0.00 | 0.02 | |
DesignProbes | 0.00 | 0.02 | 0.01 | |
DesignSignatures | 0.01 | 0.00 | 0.02 | |
DetectRepeats | 35.88 | 2.39 | 38.28 | |
DigestDNA | 0.21 | 0.00 | 0.22 | |
Disambiguate | 0.06 | 0.00 | 0.06 | |
DistanceMatrix | 0.06 | 0.00 | 0.07 | |
ExtractGenes | 61.91 | 2.42 | 64.37 | |
FindChimeras | 0.09 | 0.00 | 0.09 | |
FindGenes | 59.08 | 3.09 | 62.21 | |
FindNonCoding | 61.91 | 10.49 | 72.87 | |
FindSynteny | 1.76 | 0.06 | 1.92 | |
FormGroups | 0.07 | 0.02 | 0.08 | |
Genes-class | 58.87 | 2.67 | 61.82 | |
HEC_MI | 0.28 | 0.04 | 0.34 | |
IdConsensus | 0.36 | 0.05 | 0.42 | |
IdLengths | 0.05 | 0.00 | 0.05 | |
IdTaxa | 9.69 | 0.52 | 10.23 | |
IdentifyByRank | 0.03 | 0.01 | 0.05 | |
IndexSeqs | 0.95 | 0.02 | 0.98 | |
InvertedIndex-class | 0.70 | 0.03 | 0.75 | |
LearnNonCoding | 106.75 | 7.56 | 114.36 | |
LearnTaxa | 7.28 | 2.33 | 9.63 | |
MIQS | 0.04 | 0.05 | 0.08 | |
MMLSUM | 0.02 | 0.00 | 0.03 | |
MODELS | 0 | 0 | 0 | |
MapCharacters | 88.56 | 0.59 | 89.16 | |
MaskAlignment | 0.50 | 0.06 | 0.58 | |
MeltDNA | 0.06 | 0.00 | 0.08 | |
NNLS | 0 | 0 | 0 | |
NonCoding-class | 0.16 | 0.02 | 0.18 | |
NonCodingRNA | 0.11 | 0.00 | 0.14 | |
OrientNucleotides | 0.54 | 0.03 | 0.58 | |
PAM | 0.02 | 0.00 | 0.02 | |
PFASUM | 0.02 | 0.03 | 0.04 | |
PredictDBN | 0 | 0 | 0 | |
PredictHEC | 0.23 | 0.03 | 0.27 | |
RESTRICTION_ENZYMES | 0.00 | 0.00 | 0.02 | |
ReadDendrogram | 0.02 | 0.02 | 0.03 | |
RemoveGaps | 0 | 0 | 0 | |
ScoreAlignment | 5.06 | 0.51 | 5.58 | |
SearchDB | 0.03 | 0.04 | 0.06 | |
SearchIndex | 1.05 | 0.18 | 1.25 | |
Seqs2DB | 0.14 | 0.02 | 0.19 | |
StaggerAlignment | 14.70 | 2.22 | 16.93 | |
Synteny-class | 2.06 | 0.09 | 2.16 | |
Taxa-class | 11.10 | 0.50 | 11.59 | |
TerminalChar | 0 | 0 | 0 | |
TileSeqs | 3.22 | 0.08 | 3.30 | |
TrainingSet_16S | 2.02 | 0.03 | 2.04 | |
TreeLine | 10.29 | 0.47 | 10.77 | |
TrimDNA | 0.12 | 0.03 | 0.18 | |
WriteDendrogram | 0 | 0 | 0 | |
WriteGenes | 58.01 | 2.52 | 60.52 | |
deltaGrules | 0.00 | 0.01 | 0.03 | |
deltaGrulesRNA | 0.04 | 0.00 | 0.03 | |
deltaHrules | 0.01 | 0.00 | 0.03 | |
deltaHrulesRNA | 0.02 | 0.02 | 0.03 | |
deltaSrules | 0.04 | 0.00 | 0.06 | |
deltaSrulesRNA | 0.02 | 0.01 | 0.04 | |