Erik Wright
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/DECIPHER |
| git_branch: master |
| git_last_commit: 84592e4 |
| git_last_commit_date: 2021-10-26 12:00:41 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:19 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
To the developers/maintainers of the DECIPHER package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 467/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DECIPHER 2.23.0 (landing page) Erik Wright
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: DECIPHER |
| Version: 2.23.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DECIPHER.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings DECIPHER_2.23.0.tar.gz |
| StartedAt: 2022-03-17 18:53:07 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:06:35 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 807.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DECIPHER.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DECIPHER.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings DECIPHER_2.23.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/DECIPHER.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DECIPHER/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DECIPHER' version '2.23.0'
* 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
* checking installed package size ... NOTE
installed size is 12.2Mb
sub-directories of 1Mb or more:
R 1.1Mb
data 7.3Mb
extdata 2.2Mb
* 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 R 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
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 'deltaHrulesRNA'
Undefined global functions or variables:
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 'D:/biocbuild/bbs-3.15-bioc/R/library/DECIPHER/libs/x64/DECIPHER.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
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. 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
PredictDBN 110.14 0.59 110.74
DetectRepeats 70.47 0.61 75.90
FindNonCoding 44.54 20.05 64.59
FindGenes 44.79 2.26 47.05
LearnNonCoding 33.78 13.16 46.94
ExtractGenes 40.25 2.66 42.90
BrowseSeqs 39.08 1.04 40.18
WriteGenes 36.30 3.59 39.92
Genes-class 37.20 2.12 39.32
MapCharacters 24.92 1.28 26.20
AlignSeqs 20.67 3.42 24.09
CorrectFrameshifts 14.55 3.42 17.96
StaggerAlignment 13.80 1.73 15.53
AlignTranslation 12.61 0.63 13.24
Taxa-class 11.08 1.19 12.27
LearnTaxa 5.75 4.02 9.76
IdTaxa 9.16 0.53 9.91
DesignArray 6.42 0.07 8.21
Array2Matrix 5.36 0.01 5.38
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... 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
'D:/biocbuild/bbs-3.15-bioc/meat/DECIPHER.Rcheck/00check.log'
for details.
DECIPHER.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL DECIPHER
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'DECIPHER' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c AlignProfiles.c -o AlignProfiles.o
AlignProfiles.c: In function 'alignProfiles._omp_fn.0':
AlignProfiles.c:401:9: warning: 'lGp' may be used uninitialized in this function [-Wmaybe-uninitialized]
lGp *= tot;
~~~~^~~~~~
AlignProfiles.c:39:39: note: 'lGp' was declared here
double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS;
^~~
AlignProfiles.c:403:9: warning: 'lGs' may be used uninitialized in this function [-Wmaybe-uninitialized]
lGs *= tot;
~~~~^~~~~~
AlignProfiles.c:39:44: note: 'lGs' was declared here
double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS;
^~~
AlignProfiles.c: In function 'alignProfilesAA._omp_fn.1':
AlignProfiles.c:1220:9: warning: 'lGp' may be used uninitialized in this function [-Wmaybe-uninitialized]
lGp *= tot;
~~~~^~~~~~
AlignProfiles.c:763:39: note: 'lGp' was declared here
double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R;
^~~
AlignProfiles.c:1222:9: warning: 'lGs' may be used uninitialized in this function [-Wmaybe-uninitialized]
lGs *= tot;
~~~~^~~~~~
AlignProfiles.c:763:44: note: 'lGs' was declared here
double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R;
^~~
AlignProfiles.c: In function 'alignProfiles':
AlignProfiles.c:355:11: warning: 'subM' may be used uninitialized in this function [-Wmaybe-uninitialized]
#pragma omp parallel for private(i,j,gp,gs,S,M,GP,GS,tot,lGp,lGs) num_threads(nthreads)
^~~
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c AssignIndels.c -o AssignIndels.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c Biostrings_stubs.c -o Biostrings_stubs.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c CalculateDeltaG.c -o CalculateDeltaG.o
CalculateDeltaG.c: In function 'calculateHairpinDeltaG':
CalculateDeltaG.c:375:26: warning: 's2' may be used uninitialized in this function [-Wmaybe-uninitialized]
int i, j, k, count, s1, s2;
^~
CalculateDeltaG.c:375:22: warning: 's1' may be used uninitialized in this function [-Wmaybe-uninitialized]
int i, j, k, count, s1, s2;
^~
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c CalculateFISH.c -o CalculateFISH.o
CalculateFISH.c: In function 'calculateFISH':
CalculateFISH.c:25:23: warning: missing braces around initializer [-Wmissing-braces]
double dH_DR[4][4] = {
^
-11.5, -7.8, -7, -8.3,
{ }
-10.4, -12.8, -16.3, -9.1,
{ }
-8.6, -8, -9.3, -5.9,
{ }
-7.8, -5.5, -9, -7.8
{
};
}
CalculateFISH.c:31:23: warning: missing braces around initializer [-Wmissing-braces]
double dS_DR[4][4] = {
^
-36.4, -21.6, -19.7, -23.9,
{ }
-28.4, -31.9, -47.1, -23.5,
{ }
-22.9, -17.1, -23.2, -12.3,
{ }
-23.2, -13.5, -26.1, -21.9
{
};
}
CalculateFISH.c:37:23: warning: missing braces around initializer [-Wmissing-braces]
double dH_DD[4][4] = {
^
-7.9, -8.4, -7.8, -7.2,
{ }
-8.5, -8, -10.6, -7.8,
{ }
-8.2, -9.8, -8, -8.4,
{ }
-7.2, -8.2, -8.5, -7.9
{
};
}
CalculateFISH.c:43:23: warning: missing braces around initializer [-Wmissing-braces]
double dS_DD[4][4] = {
^
-22.2, -22.4, -21, -20.4,
{ }
-22.7, -19.9, -27.2, -21,
{ }
-22.2, -24.4, -19.9, -22.4,
{ }
-21.3, -22.2, -22.7, -22.2
{
};
}
CalculateFISH.c:49:23: warning: missing braces around initializer [-Wmissing-braces]
double dH_RR[4][4] = {
^
-6.6, -10.17, -7.65, -5.76,
{ }
-10.56, -12.21, -7.95, -7.65,
{ }
-13.37, -14.21, -12.21, -10.17,
{ }
-8.11, -13.37, -10.56, -6.6
{
};
}
CalculateFISH.c:55:23: warning: missing braces around initializer [-Wmissing-braces]
double dS_RR[4][4] = {
^
-18.38, -26.03, -19.18, -15.67,
{ }
-28.25, -30.02, -19.18, -19.18,
{ }
-35.68, -34.85, -30.02, -26.03,
{ }
-22.59, -35.68, -28.25, -18.38
{
};
}
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c ChainSegments.c -o ChainSegments.o
ChainSegments.c: In function 'chainSegments':
ChainSegments.c:422:72: warning: 'upY' may be used uninitialized in this function [-Wmaybe-uninitialized]
int minDx = 2e9, minDy = 2e9, minX = -1, minY = -2, merge = 0, upX, upY;
^~~
ChainSegments.c:422:67: warning: 'upX' may be used uninitialized in this function [-Wmaybe-uninitialized]
int minDx = 2e9, minDy = 2e9, minX = -1, minY = -2, merge = 0, upX, upY;
^~~
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c Cluster.c -o Cluster.o
Cluster.c: In function 'cluster._omp_fn.0':
Cluster.c:403:15: warning: 'minC' may be used uninitialized in this function [-Wmaybe-uninitialized]
minCol = minC;
~~~~~~~^~~~~~
Cluster.c:229:50: note: 'minC' was declared here
int k, dobj, clusterNum, minRow, minCol, index, minC, met;
^~~~
Cluster.c: In function 'cluster._omp_fn.1':
Cluster.c:418:30: warning: 'minC' may be used uninitialized in this function [-Wmaybe-uninitialized]
minCols[rowIndices[i]] = minC;
~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
Cluster.c:229:50: note: 'minC' was declared here
int k, dobj, clusterNum, minRow, minCol, index, minC, met;
^~~~
Cluster.c: In function 'cluster':
Cluster.c:229:50: warning: 'minC' may be used uninitialized in this function [-Wmaybe-uninitialized]
Cluster.c:451:168: warning: 'nDiv' may be used uninitialized in this function [-Wmaybe-uninitialized]
rans[4*(length - 1) + k] = dMatrix2[length*colIndices[minCol] - colIndices[minCol]*(colIndices[minCol] + 1)/2 + rowIndices[minRow] - colIndices[minCol]]/2 + (nDiv[minCol] - nDiv[minRow + 1])/(2*(size-2)); // col
^
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c ClusterML.c -o ClusterML.o
ClusterML.c: In function 'clusterML._omp_fn.2':
ClusterML.c:556:40: warning: 'count' may be used uninitialized in this function [-Wmaybe-uninitialized]
node[count*maxWidth*4 + i*4 + 0] += *(Ls + 0*length + j);
^~
ClusterML.c:420:6: note: 'count' was declared here
int count;
^~~~~
ClusterML.c: In function 'clusterML':
ClusterML.c:441:11: warning: 'node' may be used uninitialized in this function [-Wmaybe-uninitialized]
#pragma omp parallel for private(i,j,y_i,row,count) schedule(guided) num_threads(nthreads)
^~~
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c CommonGaps.c -o CommonGaps.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c Compositions.c -o Compositions.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c Compression.c -o Compression.o
Compression.c: In function 'nbit._omp_fn.0':
Compression.c:966:8: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (k==1 && letter >= 11) {
^
Compression.c:516:12: note: 'k' was declared here
int i, j, k, pos;
^
Compression.c:1010:12: warning: 'count' may be used uninitialized in this function [-Wmaybe-uninitialized]
count++;
~~~~~^~
Compression.c:542:29: note: 'count' was declared here
unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
^~~~~
Compression.c:1009:20: warning: 'word' may be used uninitialized in this function [-Wmaybe-uninitialized]
word = (word << 8) | (unsigned int)reorder(byte);
~~~~~~^~~~~
Compression.c:542:23: note: 'word' was declared here
unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
^~~~
Compression.c:1212:14: warning: 'rev' may be used uninitialized in this function [-Wmaybe-uninitialized]
p[c++] = rev==0 ? 254 : 255;
~~~~~~~^~~~~~~~~~~~~~~~~~~~
Compression.c:543:27: note: 'rev' was declared here
int lastTemp, currTemp, rev, len, len2, thresh = 1;
^~~
Compression.c:556:7: warning: 'lower' may be used uninitialized in this function [-Wmaybe-uninitialized]
int lower = 0;
^~~~~
Compression.c:1239:43: warning: 'lastTriplet' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (threeBitEnd > threeBitBegin && (j - lastTriplet) > 20) {
~~~^~~~~~~~~~~~~~
Compression.c:629:12: note: 'lastTriplet' was declared here
int run, lastTriplet, lastCase;
^~~~~~~~~~~
Compression.c:1029:23: warning: 'dict' may be used uninitialized in this function [-Wmaybe-uninitialized]
lastHit = dict[(word >> k) & 0xFF];
^
Compression.c:542:17: note: 'dict' was declared here
unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
^~~~
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c ConsensusSequence.c -o ConsensusSequence.o
ConsensusSequence.c: In function 'consensusProfile':
ConsensusSequence.c:1578:10: warning: 'DBN' may be used uninitialized in this function [-Wmaybe-uninitialized]
double *DBN, *s;
^~~
ConsensusSequence.c: In function 'consensusProfileAA':
ConsensusSequence.c:455:18: warning: 'lastPos' may be used uninitialized in this function [-Wmaybe-uninitialized]
*(runs + s) += weight;
^~
ConsensusSequence.c:397:23: note: 'lastPos' was declared here
int j, temp, length, lastPos, s = -1, value = -1, lastGap = start - 1;
^~~~~~~
ConsensusSequence.c:1771:10: warning: 'HEC' may be used uninitialized in this function [-Wmaybe-uninitialized]
double *HEC, *s;
^~~
ConsensusSequence.c: In function 'colScores':
ConsensusSequence.c:1938:20: warning: 'd' may be used uninitialized in this function [-Wmaybe-uninitialized]
int do_DBN, n, l, d;
^
ConsensusSequence.c:1937:10: warning: 'DBN' may be used uninitialized in this function [-Wmaybe-uninitialized]
double *DBN, *s;
^~~
ConsensusSequence.c: In function 'colScoresAA':
ConsensusSequence.c:2063:20: warning: 'd' may be used uninitialized in this function [-Wmaybe-uninitialized]
int do_HEC, n, l, d;
^
ConsensusSequence.c:2062:10: warning: 'HEC' may be used uninitialized in this function [-Wmaybe-uninitialized]
double *HEC, *s;
^~~
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c ConsolidateGaps.c -o ConsolidateGaps.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c DesignProbes.c -o DesignProbes.o
DesignProbes.c: In function 'designProbes':
DesignProbes.c:70:20: warning: missing braces around initializer [-Wmissing-braces]
double NN[4][4] = {
^
-0.816507461,-2.5401714,-1.647430026,-1.184658548
{
,-1.854740485,-2.479102613,-2.826248182,-1.647430026
}{
,-2.48761723,-4.694133177,-2.479102613,-2.5401714
}{
,-0.495794417,-2.48761723,-1.854740485,-0.816507461
}{
};
}
DesignProbes.c:77:20: warning: missing braces around initializer [-Wmissing-braces]
double PM[4][4] = {
^
-0.141370102,-0.439805276,-0.285236035,-0.205111781
{
,-0.321129768,-0.429231826,-0.48933661,-0.285236035
}{
,-0.430706047,-0.812742218,-0.429231826,-0.439805276
}{
,-0.085841845,-0.430706047,-0.321129768,-0.141370102
}{
};
}
DesignProbes.c:84:27: warning: missing braces around initializer [-Wmissing-braces]
double sMM[4][5][5][4] = {
^
0,0,0,0
{{{
,1.545032445,1.254355018,1.491691514,1.329138183
}{
,1.150635633,0.582415494,1.075877275,1.187937642
}{
,1.203555051,1.001540513,0.864287715,0.717125848
}{
,0.75,0.65,0.69,0.78
}{
,0.630005348,0.18553379,0.730763505,0.709272397
-
}},{{
,0,0,0,0
}{
,0.856582783,-0.143236405,0.716721488,0.603652831
}{
,0.851622883,0.653168672,0.676545316,1.187937642
}{
,0.75,0.65,0.69,0.78
}{
,1.231861002,0.746214538,1.087821916,0.989140748
-
}},{{
,1.822113278,1.270687029,1.336192565,1.364584949
}{
,0,0,0,0
}{
,1.443665704,1.385046493,1.256013166,1.329138183
}{
,0.75,0.65,0.69,0.78
}{
,1.478009492,0.882097231,1.20450984,1.061002478
-
}},{{
,1.496720812,0.846496194,0.967868114,0.989140748
}{
,0.766581547,-0.024857805,0.50754303,0.709272397
}{
,0,0,0,0
}{
,0.75,0.65,0.69,0.78
}{
,0.75,0.65,0.69,0.78
-
}},{{
,0.75,0.65,0.69,0.78
}{
,0.75,0.65,0.69,0.78
}{
,0.76,0.65,0.69,0.78
}{
,0,0,0,0
}{
,0,0,0,0
-
}}},{{{
,1.295827995,0.84547091,0.91019099,1.256013166
}{
,0.755889609,0.241428373,0.396379912,0.676545316
}{
,0.99945386,0.740323132,0.435659206,0.864287715
}{
,0.65,0.55,0.48,0.69
}{
,0.843147406,0.101248351,0.49063599,0.50754303
-
}},{{
,0,0,0,0
}{
,1.0651638,0.249934344,0.699352949,0.716721488
}{
,0.871921533,0.59458138,0.396379912,1.075877275
}{
,0.65,0.56,0.49,0.69
}{
,1.07531714,0.318907854,0.653287717,0.967868114
-
}},{{
,1.099899195,0.730184613,0.661798984,1.336192565
}{
,0,0,0,0
}{
,1.45897431,1.318532145,0.91019099,1.491691514
}{
,0.65,0.56,0.49,0.69
}{
,1.242135174,0.894838095,1.108555445,1.20450984
-
}},{{
,0.911428974,0.524430101,0.653287717,1.087821916
}{
,0.503209827,0.274849491,0.49063599,0.730763505
}{
,0,0,0,0
}{
,0.65,0.55,0.48,0.69
}{
,0.65,0.55,0.48,0.69
-
}},{{
,0.65,0.56,0.49,0.69
}{
,0.65,0.56,0.49,0.69
}{
,0.65,0.55,0.48,0.69
}{
,0,0,0,0
}{
,0,0,0,0
-
}}},{{{
,1.100661785,0.969784756,1.318532145,1.385046493
}{
,0.565895968,-0.060347902,0.59458138,0.653168672
}{
,0.782168488,0.788161238,0.740323132,1.001540513
}{
,0.68,0.46,0.55,0.65
}{
,0.468913405,-0.469855984,0.274849491,-0.024857805
-
}},{{
,0,0,0,0
}{
,0.258195131,-0.70438632,0.249934344,-0.143236405
}{
,0.502914193,-0.060347902,0.241428373,0.582415494
}{
,0.68,0.47,0.56,0.65
}{
,0.584083861,0.258975454,0.524430101,0.846496194
-
}},{{
,0.968040559,0.797499702,0.730184613,1.270687029
}{
,0,0,0,0
}{
,1.081040749,0.969784756,0.84547091,1.254355018
}{
,0.68,0.47,0.56,0.65
}{
,1.048553951,0.728354541,0.894838095,0.882097231
-
}},{{
,0.88611252,0.258975454,0.318907854,0.746214538
}{
,0.239520858,-0.469855984,0.101248351,0.18553379
}{
,0,0,0,0
}{
,0.68,0.46,0.55,0.65
}{
,0.68,0.46,0.55,0.65
-
}},{{
,0.68,0.47,0.56,0.65
}{
,0.68,0.47,0.56,0.65
}{
,0.68,0.46,0.55,0.65
}{
,0,0,0,0
}{
,0,0,0,0
-
}}},{{{
,1.566899704,1.081040749,1.45897431,1.443665704
}{
,0.976725675,0.502914193,0.871921533,0.851622883
}{
,1.482046826,0.782168488,0.99945386,1.203555051
}{
,0.85,0.68,0.65,0.76
}{
,0.798628781,0.239520858,0.503209827,0.766581547
-
}},{{
,0,0,0,0
}{
,1.141098246,0.258195131,1.0651638,0.856582783
}{
,0.976725675,0.565895968,0.755889609,1.150635633
}{
,0.85,0.68,0.65,0.75
}{
,1.125403302,0.88611252,0.911428974,1.496720812
-
}},{{
,1.68169282,0.968040559,1.099899195,1.822113278
}{
,0,0,0,0
}{
,1.566899704,1.100661785,1.295827995,1.545032445
}{
,0.85,0.68,0.65,0.75
}{
,1.35948517,1.048553951,1.242135174,1.478009492
-
}},{{
,1.125403302,0.584083861,1.07531714,1.231861002
}{
,0.798628781,0.468913405,0.843147406,0.630005348
}{
,0,0,0,0
}{
,0.85,0.68,0.65,0.75
}{
,0.85,0.68,0.65,0.75
-
}},{{
,0.85,0.68,0.65,0.75
}{
,0.85,0.68,0.65,0.75
}{
,0.85,0.68,0.65,0.75
}{
,0,0,0,0
}{
};
}}}
DesignProbes.c: In function 'designProbes._omp_fn.0':
DesignProbes.c:834:29: warning: 'lastCycle' may be used uninitialized in this function [-Wmaybe-uninitialized]
cycles += lastCycle - thisCycle;
~~~~~~~~~~^~~~~~~~~~~
DesignProbes.c:267:37: note: 'lastCycle' was declared here
int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles;
^~~~~~~~~
DesignProbes.c:834:29: warning: 'thisCycle' may be used uninitialized in this function [-Wmaybe-uninitialized]
cycles += lastCycle - thisCycle;
~~~~~~~~~~^~~~~~~~~~~
DesignProbes.c:267:48: note: 'thisCycle' was declared here
int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles;
^~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c Diff.c -o Diff.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c DistanceMatrix.c -o DistanceMatrix.o
DistanceMatrix.c: In function 'firstSeqsPosEqual':
DistanceMatrix.c:625:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (!ci)
^~
DistanceMatrix.c:628:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
while (i < ex) {
^~~~~
DistanceMatrix.c:647:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (!cj)
^~
DistanceMatrix.c:650:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
while (j < ey) {
^~~~~
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c EnumerateSequence.c -o EnumerateSequence.o
EnumerateSequence.c: In function 'pop':
EnumerateSequence.c:315:8: warning: suggest parentheses around '+' in operand of '&' [-Wparentheses]
x = x + (x >> 4) & 0xF0F0F0F;
~~^~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c ExpandAmbiguities.c -o ExpandAmbiguities.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c FindFrameshifts.c -o FindFrameshifts.o
FindFrameshifts.c: In function 'findFrameshifts':
FindFrameshifts.c:376:7: warning: 'K' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (k==1) {
^
FindFrameshifts.c:372:8: warning: 'J' may be used uninitialized in this function [-Wmaybe-uninitialized]
j -= B[k*rc + j*r + i];
~~^~~~~~~~~~~~~~~~~~~~
FindFrameshifts.c:320:13: warning: 'I' may be used uninitialized in this function [-Wmaybe-uninitialized]
pos = i*3 + k + 1;
~^~
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c GeneFinding.c -o GeneFinding.o
GeneFinding.c: In function 'scoreCodonModel':
GeneFinding.c:388:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
Chars_holder x_i;
^~~
GeneFinding.c:432:29: warning: 'lastVal' may be used uninitialized in this function [-Wmaybe-uninitialized]
score += codons[lastVal*64 + val];
~~~~~~~^~~
GeneFinding.c: In function 'startCodonModel':
GeneFinding.c:793:31: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
val += 16*getBaseRC(x_i.ptr[j]);
^
GeneFinding.c: In function 'scoreStartCodonModel':
GeneFinding.c:894:31: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
val += 16*getBaseRC(x_i.ptr[j]);
^
GeneFinding.c: In function 'initialCodonModel':
GeneFinding.c:928:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
Chars_holder x_i;
^~~
GeneFinding.c: In function 'scoreInitialCodonModel':
GeneFinding.c:1031:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
Chars_holder x_i;
^~~
GeneFinding.c: In function 'terminationCodonModel':
GeneFinding.c:1092:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
Chars_holder x_i;
^~~
GeneFinding.c: In function 'scoreTerminationCodonModel':
GeneFinding.c:1188:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
Chars_holder x_i;
^~~
GeneFinding.c: In function 'getRegion':
GeneFinding.c:1286:21: warning: 'x_i.length' may be used uninitialized in this function [-Wmaybe-uninitialized]
(s==0 && j >= 0 && j + w <= x_i.length)) {
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
GeneFinding.c:1252:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
Chars_holder x_i;
^~~
GeneFinding.c: In function 'autocorrelationModel':
GeneFinding.c:1350:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
Chars_holder x_i;
^~~
GeneFinding.c: In function 'scoreAutocorrelationModel':
GeneFinding.c:1461:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
Chars_holder x_i;
^~~
GeneFinding.c: In function 'couplingModel':
GeneFinding.c:1573:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
Chars_holder x_i;
^~~
GeneFinding.c: In function 'scoreCouplingModel':
GeneFinding.c:1681:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
Chars_holder x_i;
^~~
GeneFinding.c: In function 'nucleotideBiasModel':
GeneFinding.c:1788:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
Chars_holder x_i;
^~~
GeneFinding.c: In function 'scoreNucleotideBiasModel':
GeneFinding.c:1882:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
Chars_holder x_i;
^~~
GeneFinding.c: In function 'upstreamMotifModel':
GeneFinding.c:1990:42: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
val += mult[k - 1]*getBaseRC(x_i.ptr[j + k - 1]);
^
GeneFinding.c: In function 'scoreUpstreamMotifModel':
GeneFinding.c:2090:42: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
val += mult[k - 1]*getBaseRC(x_i.ptr[j + k - 1]);
^
GeneFinding.c: In function 'scoreRunLengthModel':
GeneFinding.c:2276:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
Chars_holder x_i;
^~~
GeneFinding.c: In function 'stopCodonModel':
GeneFinding.c:2421:31: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
val += 16*getBaseRC(x_i.ptr[j]);
^
GeneFinding.c: In function 'scoreStopCodonModel':
GeneFinding.c:2522:31: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
val += 16*getBaseRC(x_i.ptr[j]);
^
GeneFinding.c: In function 'codonFrequencies':
GeneFinding.c:2554:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
Chars_holder x_i;
^~~
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c GetPools.c -o GetPools.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c Import.c -o Import.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c InformationContent.c -o InformationContent.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c InsertGaps.c -o InsertGaps.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c IntDist.c -o IntDist.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c MeltPolymer.c -o MeltPolymer.o
MeltPolymer.c: In function 'meltPolymer':
MeltPolymer.c:79:20: warning: missing braces around initializer [-Wmissing-braces]
double dH[4][4] = {
^
-7.9,-8.4,-7.8,-7.2
{
,-8.5,-8.0,-10.6,-7.8
}{
,-8.2,-9.8,-8.0,-8.4
}{
,-7.2,-8.2,-8.5,-7.9
}{
};
}
MeltPolymer.c:88:20: warning: missing braces around initializer [-Wmissing-braces]
double dS[4][4] = {
^
-22.2,-22.4,-21.0,-20.4
{
,-22.7,-19.9,-27.2,-21.0
}{
,-22.2,-24.4,-19.9,-22.4
}{
,-21.3,-22.2,-22.7,-22.2
}{
};
}
MeltPolymer.c:54:10: warning: 'rans' may be used uninitialized in this function [-Wmaybe-uninitialized]
double *rans;
^~~~
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c MovingAverage.c -o MovingAverage.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c MultiMatch.c -o MultiMatch.o
MultiMatch.c: In function 'intMatchSelfOnce':
MultiMatch.c:866:21: warning: variable 'start' set but not used [-Wunused-but-set-variable]
int i, j, k, temp, start = 0;
^~~~~
In file included from D:/biocbuild/bbs-3.15-bioc/R/include/Rdefines.h:41,
from MultiMatch.c:11:
MultiMatch.c: In function 'matchLists':
D:/biocbuild/bbs-3.15-bioc/R/include/Rinternals.h:885:16: warning: 'utilsPackage' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define eval Rf_eval
^~~~~~~
MultiMatch.c:244:24: note: 'utilsPackage' was declared here
SEXP percentComplete, utilsPackage;
^~~~~~~~~~~~
In file included from D:/biocbuild/bbs-3.15-bioc/R/include/Rdefines.h:41,
from MultiMatch.c:11:
D:/biocbuild/bbs-3.15-bioc/R/include/Rinternals.h:885:16: warning: 'percentComplete' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define eval Rf_eval
^~~~~~~
MultiMatch.c:244:7: note: 'percentComplete' was declared here
SEXP percentComplete, utilsPackage;
^~~~~~~~~~~~~~~
MultiMatch.c:327:12: warning: 'rPercentComplete' may be used uninitialized in this function [-Wmaybe-uninitialized]
before = *rPercentComplete;
~~~~~~~^~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c NNLS.c -o NNLS.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c Order.c -o Order.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c PredictDBN.c -o PredictDBN.o
PredictDBN.c: In function 'predictDBN':
PredictDBN.c:869:29: warning: 'prev' may be used uninitialized in this function [-Wmaybe-uninitialized]
range2[0] = nucs[pos[prev]];// + 1;
^
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c PredictHEC.c -o PredictHEC.o
PredictHEC.c: In function 'predictHEC':
PredictHEC.c:255:4: warning: 'ans' may be used uninitialized in this function [-Wmaybe-uninitialized]
SET_VECTOR_ELT(ret, i, ans);
^~~~~~~~~~~~~~~~~~~~~~~~~~~
PredictHEC.c:42:8: warning: 'states' may be used uninitialized in this function [-Wmaybe-uninitialized]
char *states;
^~~~~~
PredictHEC.c:41:24: warning: 'rans' may be used uninitialized in this function [-Wmaybe-uninitialized]
double H, E, C, sum, *rans;
^~~~
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c R_init_decipher.c -o R_init_decipher.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c RemoveGaps.c -o RemoveGaps.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c ReplaceChars.c -o ReplaceChars.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c S4Vectors_stubs.c -o S4Vectors_stubs.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c TerminalMismatch.c -o TerminalMismatch.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c Translate.c -o Translate.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c VectorSums.c -o VectorSums.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c XVector_stubs.c -o XVector_stubs.o
C:/rtools40/mingw64/bin/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 CommonGaps.o Compositions.o Compression.o ConsensusSequence.o ConsolidateGaps.o DesignProbes.o Diff.o DistanceMatrix.o EnumerateSequence.o ExpandAmbiguities.o FindFrameshifts.o GeneFinding.o GetPools.o Import.o InformationContent.o InsertGaps.o IntDist.o MeltPolymer.o MovingAverage.o MultiMatch.o NNLS.o Order.o PredictDBN.o PredictHEC.o R_init_decipher.o RemoveGaps.o ReplaceChars.o S4Vectors_stubs.o TerminalMismatch.o Translate.o VectorSums.o XVector_stubs.o -fopenmp -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-DECIPHER/00new/DECIPHER/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'DECIPHER'
finding HTML links ... done
AA_REDUCED html
Add2DB html
AdjustAlignment html
AlignDB html
AlignProfiles html
AlignSeqs html
AlignSynteny html
AlignTranslation html
AmplifyDNA html
Array2Matrix html
BrowseDB html
BrowseSeqs html
CalculateEfficiencyArray html
CalculateEfficiencyFISH html
CalculateEfficiencyPCR html
Codec html
ConsensusSequence html
Cophenetic html
CorrectFrameshifts html
CreateChimeras html
DB2Seqs html
DECIPHER-package html
DesignArray html
DesignPrimers html
DesignProbes html
DesignSignatures html
DetectRepeats html
DigestDNA html
Disambiguate html
DistanceMatrix html
ExtractGenes html
FindChimeras html
FindGenes html
FindNonCoding html
FindSynteny html
FormGroups html
Genes-class html
HEC_MI html
IdClusters html
IdConsensus html
IdLengths html
IdTaxa html
IdentifyByRank html
LearnNonCoding html
LearnTaxa html
MIQS html
MODELS html
MapCharacters html
MaskAlignment html
MeltDNA html
NNLS html
NonCoding-class html
NonCodingRNA html
OrientNucleotides html
PFASUM html
PredictDBN html
PredictHEC html
RESTRICTION_ENZYMES html
ReadDendrogram html
RemoveGaps html
SearchDB html
Seqs2DB html
StaggerAlignment html
Synteny-class html
Taxa-class html
TerminalChar html
TileSeqs html
TrainingSet_16S html
TrimDNA html
WriteDendrogram html
WriteGenes html
deltaGrules html
deltaHrules html
deltaHrulesRNA html
deltaSrules html
deltaSrulesRNA html
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'MetaboAnnotation' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'miaSim' is missing or broken
done
DECIPHER.Rcheck/DECIPHER-Ex.timings
| name | user | system | elapsed | |
| AA_REDUCED | 0.03 | 0.00 | 0.03 | |
| Add2DB | 0.20 | 0.01 | 0.22 | |
| AdjustAlignment | 0.19 | 0.00 | 0.19 | |
| AlignDB | 0.84 | 0.09 | 0.94 | |
| AlignProfiles | 0.95 | 0.05 | 1.00 | |
| AlignSeqs | 20.67 | 3.42 | 24.09 | |
| AlignSynteny | 2.02 | 0.14 | 2.16 | |
| AlignTranslation | 12.61 | 0.63 | 13.24 | |
| AmplifyDNA | 0.01 | 0.00 | 0.01 | |
| Array2Matrix | 5.36 | 0.01 | 5.38 | |
| BrowseDB | 0.03 | 0.00 | 0.03 | |
| BrowseSeqs | 39.08 | 1.04 | 40.18 | |
| CalculateEfficiencyArray | 0.02 | 0.00 | 0.02 | |
| CalculateEfficiencyFISH | 0.01 | 0.00 | 0.02 | |
| CalculateEfficiencyPCR | 0 | 0 | 0 | |
| Codec | 0.97 | 0.00 | 0.96 | |
| ConsensusSequence | 0.14 | 0.00 | 0.15 | |
| Cophenetic | 0.89 | 0.00 | 0.89 | |
| CorrectFrameshifts | 14.55 | 3.42 | 17.96 | |
| CreateChimeras | 0.75 | 0.00 | 0.75 | |
| DB2Seqs | 0.00 | 0.01 | 0.04 | |
| DesignArray | 6.42 | 0.07 | 8.21 | |
| DesignPrimers | 0 | 0 | 0 | |
| DesignProbes | 0 | 0 | 0 | |
| DesignSignatures | 0 | 0 | 0 | |
| DetectRepeats | 70.47 | 0.61 | 75.90 | |
| DigestDNA | 0.09 | 0.01 | 0.10 | |
| Disambiguate | 0.04 | 0.00 | 0.04 | |
| DistanceMatrix | 0.03 | 0.00 | 0.03 | |
| ExtractGenes | 40.25 | 2.66 | 42.90 | |
| FindChimeras | 0.07 | 0.00 | 0.08 | |
| FindGenes | 44.79 | 2.26 | 47.05 | |
| FindNonCoding | 44.54 | 20.05 | 64.59 | |
| FindSynteny | 0.96 | 0.00 | 0.96 | |
| FormGroups | 0.03 | 0.00 | 0.03 | |
| Genes-class | 37.20 | 2.12 | 39.32 | |
| HEC_MI | 0.20 | 0.02 | 0.22 | |
| IdClusters | 0.36 | 0.00 | 0.36 | |
| IdConsensus | 0.62 | 0.06 | 0.69 | |
| IdLengths | 0.02 | 0.00 | 0.01 | |
| IdTaxa | 9.16 | 0.53 | 9.91 | |
| IdentifyByRank | 0.03 | 0.00 | 0.03 | |
| LearnNonCoding | 33.78 | 13.16 | 46.94 | |
| LearnTaxa | 5.75 | 4.02 | 9.76 | |
| MIQS | 0.03 | 0.01 | 0.05 | |
| MODELS | 0 | 0 | 0 | |
| MapCharacters | 24.92 | 1.28 | 26.20 | |
| MaskAlignment | 0.49 | 0.03 | 0.52 | |
| MeltDNA | 0.04 | 0.00 | 0.04 | |
| NNLS | 0.05 | 0.00 | 0.05 | |
| NonCoding-class | 0.03 | 0.02 | 0.05 | |
| NonCodingRNA | 0.09 | 0.02 | 0.11 | |
| OrientNucleotides | 0.85 | 0.00 | 0.84 | |
| PFASUM | 0.01 | 0.01 | 0.03 | |
| PredictDBN | 110.14 | 0.59 | 110.74 | |
| PredictHEC | 0.25 | 0.02 | 0.27 | |
| RESTRICTION_ENZYMES | 0 | 0 | 0 | |
| ReadDendrogram | 0.05 | 0.03 | 0.08 | |
| RemoveGaps | 0.01 | 0.00 | 0.01 | |
| SearchDB | 0.03 | 0.00 | 0.03 | |
| Seqs2DB | 0.09 | 0.02 | 0.11 | |
| StaggerAlignment | 13.80 | 1.73 | 15.53 | |
| Synteny-class | 1.75 | 0.00 | 1.75 | |
| Taxa-class | 11.08 | 1.19 | 12.27 | |
| TerminalChar | 0.01 | 0.00 | 0.01 | |
| TileSeqs | 2.99 | 0.00 | 2.99 | |
| TrainingSet_16S | 2.40 | 0.03 | 2.43 | |
| TrimDNA | 0.07 | 0.00 | 0.07 | |
| WriteDendrogram | 0.01 | 0.00 | 0.01 | |
| WriteGenes | 36.30 | 3.59 | 39.92 | |
| deltaGrules | 0.00 | 0.02 | 0.02 | |
| deltaHrules | 0.01 | 0.00 | 0.01 | |
| deltaHrulesRNA | 0.02 | 0.02 | 0.04 | |
| deltaSrules | 0.05 | 0.00 | 0.04 | |
| deltaSrulesRNA | 0.01 | 0.00 | 0.02 | |