| Back to Build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-02-27 02:34:32 -0000 (Mon, 27 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4259 |
| 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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 479/2169 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DECIPHER 2.27.0 (landing page) Erik Wright
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: DECIPHER |
| Version: 2.27.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:DECIPHER.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings DECIPHER_2.27.0.tar.gz |
| StartedAt: 2023-02-24 09:53:35 -0000 (Fri, 24 Feb 2023) |
| EndedAt: 2023-02-24 10:31:51 -0000 (Fri, 24 Feb 2023) |
| EllapsedTime: 2295.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: DECIPHER.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:DECIPHER.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings DECIPHER_2.27.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/DECIPHER.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘DECIPHER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DECIPHER’ version ‘2.27.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘DECIPHER’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking installed package size ... NOTE
installed size is 12.7Mb
sub-directories of 1Mb or more:
R 1.4Mb
data 7.3Mb
extdata 2.3Mb
libs 1.3Mb
* 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’
TreeLine: multiple local function definitions for ‘.minimize’ with
different formal arguments
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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘DECIPHER-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: LearnNonCoding
> ### Title: Learn a Non-Coding RNA Model
> ### Aliases: LearnNonCoding
>
> ### ** Examples
>
> # import a family of non-coding RNAs
> fas_path <- system.file("extdata",
+ "IhtA.fas",
+ package="DECIPHER")
> rna <- readRNAStringSet(fas_path)
> rna
RNAStringSet object of length 27:
width seq names
[1] 103 AAGAUGAUAUUCUGCGCCAUGGA...UGAUUGUUGUUUUCUUGGCUUU KE360988.1/6443-6...
[2] 105 AAGAUGAUAUUCUCCGCCGUGGA...AACUUUAUGUUUUCUUGGCUUU AE002161.1/54676-...
[3] 107 AAGUUGGUAUUCUAACGCCAUGG...UAUCUCCGGUUCUCUUGGCUUU AE001273.1/773281...
[4] 107 AAGUUGGUAUUCUAACGCCAUGG...UGUCUCCAGUUCUCUUGGCUUU AE002160.2/53054-...
[5] 103 AAGAUGAUAUUCUACGCCAUGGA...UGAUUGUUGUUUUCUUGGCUUU AE015925.1/52097-...
... ... ...
[23] 107 AAGUUGGUAUUCUAACGCCAUGG...UAUCUCCGGUUCUCUUGGCUUU CP006674.1 Chlamy...
[24] 103 AAGAUGAUAUUCUGCGCCAUGGA...UGAUUGUUGUUUUCUUGGCUUU KE356008.1 Chlamy...
[25] 108 AAGUUGGUAUUCUAACGCCAUGG...UAUCUCCGGUUCUCUUGGCUUU CVNC01000001.1 Ch...
[26] 103 AAGAUGAUAUUCUGCGCCAUGGA...UGAUUGUUGUUUUCUUGGCUUU AP006861.1 Chlamy...
[27] 101 AAGAUGAUAUUCUACGCCAUGGA...AUGAUGUUGUUUUCUUGGCUUU CP015840.1 Chlamy...
>
> # align the sequences
> RNA <- AlignSeqs(rna)
Determining distance matrix based on shared 7-mers:
================================================================================
Time difference of 0 secs
Clustering into groups by similarity:
================================================================================
Time difference of 0.01 secs
Aligning Sequences:
================================================================================
Time difference of 0.19 secs
Iteration 1 of 2:
Determining distance matrix based on alignment:
================================================================================
Time difference of 0 secs
Reclustering into groups by similarity:
================================================================================
Time difference of 0.01 secs
Realigning Sequences:
================================================================================
Time difference of 0.1 secs
Iteration 2 of 2:
Determining distance matrix based on alignment:
================================================================================
Time difference of 0 secs
Reclustering into groups by similarity:
================================================================================
Time difference of 0.01 secs
Realigning Sequences:
================================================================================
Time difference of 0.02 secs
> RNA
RNAStringSet object of length 27:
width seq names
[1] 113 AAGAUGAUAUUCUG-CGCCAUGG...GAUUGU-UGUUUUCUUGGCUUU KE360988.1/6443-6...
[2] 113 AAGAUGAUAUUCUC-CGCCGUGG...AACUUUAUGUUUUCUUGGCUUU AE002161.1/54676-...
[3] 113 AAGUUGGUAUUCUAACGCCAUGG...--UCUCCGGUUCUCUUGGCUUU AE001273.1/773281...
[4] 113 AAGUUGGUAUUCUAACGCCAUGG...--UCUCCAGUUCUCUUGGCUUU AE002160.2/53054-...
[5] 113 AAGAUGAUAUUCUA-CGCCAUGG...GAUUGU-UGUUUUCUUGGCUUU AE015925.1/52097-...
... ... ...
[23] 113 AAGUUGGUAUUCUAACGCCAUGG...--UCUCCGGUUCUCUUGGCUUU CP006674.1 Chlamy...
[24] 113 AAGAUGAUAUUCUG-CGCCAUGG...GAUUGU-UGUUUUCUUGGCUUU KE356008.1 Chlamy...
[25] 113 AAGUUGGUAUUCUAACGCCAUGG...--UCUCCGGUUCUCUUGGCUUU CVNC01000001.1 Ch...
[26] 113 AAGAUGAUAUUCUG-CGCCAUGG...GAUUGU-UGUUUUCUUGGCUUU AP006861.1 Chlamy...
[27] 113 AAGAUGAUAUUCUA-CGCCAUGG...GAU-GU-UGUUUUCUUGGCUUU CP015840.1 Chlamy...
>
> y <- LearnNonCoding(RNA)
Killed
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘ArtOfAlignmentInR.Rnw’... OK
‘ClassifySequences.Rnw’... OK
‘ClusteringSequences.Rnw’... OK
‘DECIPHERing.Rnw’... OK
‘DesignMicroarray.Rnw’... OK
‘DesignPrimers.Rnw’... OK
‘DesignProbes.Rnw’... OK
‘DesignSignatures.Rnw’... OK
‘FindChimeras.Rnw’... OK
‘FindingGenes.Rnw’... OK
‘FindingNonCodingRNAs.Rnw’... failed to complete the test
‘GrowingTrees.Rnw’... OK
‘RepeatRepeat.Rnw’... OK
ERROR
Errors in running code in vignettes:
when running code in ‘FindingNonCodingRNAs.Rnw’
...
[46] "5'_ureB-RF02514"
> x[[length(x) + 1]] <- y
> names(x)[length(x)] <- "IhtA"
> rnas <- FindNonCoding(x, genome)
===Killed
... incomplete output. Crash?
* checking re-building of vignette outputs ... NOTE
Error(s) in re-building vignettes:
--- re-building ‘ArtOfAlignmentInR.Rnw’ using Sweave
Loading required package: Biostrings
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:base’:
I, expand.grid, unname
Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomeInfoDb
Attaching package: ‘Biostrings’
The following object is masked from ‘package:base’:
strsplit
Loading required package: RSQLite
Loading required package: parallel
--- finished re-building ‘ArtOfAlignmentInR.Rnw’
--- re-building ‘ClassifySequences.Rnw’ using Sweave
Loading required package: Biostrings
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:base’:
I, expand.grid, unname
Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomeInfoDb
Attaching package: ‘Biostrings’
The following object is masked from ‘package:base’:
strsplit
Loading required package: RSQLite
Loading required package: parallel
Warning in par(p) : argument 1 does not name a graphical parameter
--- finished re-building ‘ClassifySequences.Rnw’
--- re-building ‘ClusteringSequences.Rnw’ using Sweave
Loading required package: Biostrings
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:base’:
I, expand.grid, unname
Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomeInfoDb
Attaching package: ‘Biostrings’
The following object is masked from ‘package:base’:
strsplit
Loading required package: RSQLite
Loading required package: parallel
--- finished re-building ‘ClusteringSequences.Rnw’
--- re-building ‘DECIPHERing.Rnw’ using Sweave
Loading required package: Biostrings
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:base’:
I, expand.grid, unname
Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomeInfoDb
Attaching package: ‘Biostrings’
The following object is masked from ‘package:base’:
strsplit
Loading required package: RSQLite
Loading required package: parallel
--- finished re-building ‘DECIPHERing.Rnw’
--- re-building ‘DesignMicroarray.Rnw’ using Sweave
Loading required package: Biostrings
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:base’:
I, expand.grid, unname
Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomeInfoDb
Attaching package: ‘Biostrings’
The following object is masked from ‘package:base’:
strsplit
Loading required package: RSQLite
Loading required package: parallel
--- finished re-building ‘DesignMicroarray.Rnw’
--- re-building ‘DesignPrimers.Rnw’ using Sweave
Loading required package: Biostrings
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:base’:
I, expand.grid, unname
Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomeInfoDb
Attaching package: ‘Biostrings’
The following object is masked from ‘package:base’:
strsplit
Loading required package: RSQLite
Loading required package: parallel
--- finished re-building ‘DesignPrimers.Rnw’
--- re-building ‘DesignProbes.Rnw’ using Sweave
Loading required package: Biostrings
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:base’:
I, expand.grid, unname
Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomeInfoDb
Attaching package: ‘Biostrings’
The following object is masked from ‘package:base’:
strsplit
Loading required package: RSQLite
Loading required package: parallel
--- finished re-building ‘DesignProbes.Rnw’
--- re-building ‘DesignSignatures.Rnw’ using Sweave
Loading required package: Biostrings
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:base’:
I, expand.grid, unname
Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomeInfoDb
Attaching package: ‘Biostrings’
The following object is masked from ‘package:base’:
strsplit
Loading required package: RSQLite
Loading required package: parallel
--- finished re-building ‘DesignSignatures.Rnw’
--- re-building ‘FindChimeras.Rnw’ using Sweave
Loading required package: Biostrings
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:base’:
I, expand.grid, unname
Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomeInfoDb
Attaching package: ‘Biostrings’
The following object is masked from ‘package:base’:
strsplit
Loading required package: RSQLite
Loading required package: parallel
--- finished re-building ‘FindChimeras.Rnw’
--- re-building ‘FindingGenes.Rnw’ using Sweave
Loading required package: Biostrings
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:base’:
I, expand.grid, unname
Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomeInfoDb
Attaching package: ‘Biostrings’
The following object is masked from ‘package:base’:
strsplit
Loading required package: RSQLite
Loading required package: parallel
--- finished re-building ‘FindingGenes.Rnw’
--- re-building ‘FindingNonCodingRNAs.Rnw’ using Sweave
Loading required package: Biostrings
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:base’:
I, expand.grid, unname
Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomeInfoDb
Attaching package: ‘Biostrings’
The following object is masked from ‘package:base’:
strsplit
Loading required package: RSQLite
Loading required package: parallel
Killed
--- re-building ‘GrowingTrees.Rnw’ using Sweave
Loading required package: Biostrings
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:base’:
I, expand.grid, unname
Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomeInfoDb
Attaching package: ‘Biostrings’
The following object is masked from ‘package:base’:
strsplit
Loading required package: RSQLite
Loading required package: parallel
--- finished re-building ‘GrowingTrees.Rnw’
--- re-building ‘RepeatRepeat.Rnw’ using Sweave
Loading required package: Biostrings
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:base’:
I, expand.grid, unname
Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomeInfoDb
Attaching package: ‘Biostrings’
The following object is masked from ‘package:base’:
strsplit
Loading required package: RSQLite
Loading required package: parallel
--- finished re-building ‘RepeatRepeat.Rnw’
SUMMARY: processing the following file failed:
‘FindingNonCodingRNAs.Rnw’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 4 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/DECIPHER.Rcheck/00check.log’
for details.
DECIPHER.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL DECIPHER
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘DECIPHER’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c AlignProfiles.c -o AlignProfiles.o
AlignProfiles.c: In function ‘alignProfiles._omp_fn.0’:
AlignProfiles.c:424:37: warning: ‘lGp’ may be used uninitialized in this function [-Wmaybe-uninitialized]
424 | 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:426:37: warning: ‘lGs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
426 | 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: In function ‘alignProfilesAA._omp_fn.0’:
AlignProfiles.c:1266:37: warning: ‘lGp’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1266 | lGp *= tot;
| ~~~~^~~~~~
AlignProfiles.c:808:46: note: ‘lGp’ was declared here
808 | double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R, temp, avgM = 0;
| ^~~
AlignProfiles.c:1268:37: warning: ‘lGs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1268 | lGs *= tot;
| ~~~~^~~~~~
AlignProfiles.c:808:51: note: ‘lGs’ was declared here
808 | double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R, temp, avgM = 0;
| ^~~
AlignProfiles.c: In function ‘alignProfiles’:
AlignProfiles.c:378:25: warning: ‘subM’ may be used uninitialized in this function [-Wmaybe-uninitialized]
378 | #pragma omp parallel for private(i,j,gp,gs,S,M,GP,GS,tot,lGp,lGs,temp) reduction(+:totM,avgM) num_threads(nthreads)
| ^~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c AssignIndels.c -o AssignIndels.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c CalculateDeltaG.c -o CalculateDeltaG.o
CalculateDeltaG.c: In function ‘calculateHairpinDeltaG’:
CalculateDeltaG.c:463:49: warning: ‘s2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
463 | if ((!((s1 == 4) && (s2 == 4)) || j >= a[i]) && count > 3) {
| ~~~~^~~~~
CalculateDeltaG.c:463:36: warning: ‘s1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
463 | if ((!((s1 == 4) && (s2 == 4)) || j >= a[i]) && count > 3) {
| ~~~~^~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -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"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c ChainSegments.c -o ChainSegments.o
ChainSegments.c: In function ‘chainSegments’:
ChainSegments.c:500:49: warning: ‘upY’ may be used uninitialized in this function [-Wmaybe-uninitialized]
500 | if (minX == minY && upX == upY) {
| ~~~~^~~~~~
ChainSegments.c:500:49: warning: ‘upX’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c Cluster.c -o Cluster.o
Cluster.c: In function ‘cluster._omp_fn.0’:
Cluster.c:403:50: warning: ‘minC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
403 | minCs[i] = minC;
| ~~~~~~~~~^~~~~~
Cluster.c:231:57: note: ‘minC’ was declared here
231 | int k, dobj, clusterNum, minRow, minCol, index, minC, met;
| ^~~~
Cluster.c: In function ‘cluster._omp_fn.1’:
Cluster.c:427:72: warning: ‘minC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
427 | minCols[rowIndices[i]] = minC;
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
Cluster.c:231:57: note: ‘minC’ was declared here
231 | int k, dobj, clusterNum, minRow, minCol, index, minC, met;
| ^~~~
Cluster.c: In function ‘cluster’:
Cluster.c:449:66: warning: ‘minC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
449 | rans[1*(length - 1) + k] = *(colNums + colIndices[minCol]); // column merged
| ^
Cluster.c:739:37: warning: ‘nDiv’ may be used uninitialized in this function [-Wmaybe-uninitialized]
739 | nDiv[i] = nDiv[i + 1];
| ^
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c ClusterML.c -o ClusterML.o
ClusterML.c:5666:13: warning: ‘L_unknown_5_SIMD’ defined but not used [-Wunused-function]
5666 | static void L_unknown_5_SIMD(double *__restrict Ls, const int i3, const int i1, const int i2, const double *P1, const double *P2, const double epsilon, const double inv_epsilon, const int root)
| ^~~~~~~~~~~~~~~~
ClusterML.c:5064:13: warning: ‘L_unknown_SIMD’ defined but not used [-Wunused-function]
5064 | static void L_unknown_SIMD(double *__restrict Ls, const int i3, const int i1, const int i2, const double *P1, const double *P2, const double epsilon, const double inv_epsilon, const int root)
| ^~~~~~~~~~~~~~
ClusterML.c: In function ‘clusterML’:
ClusterML.c:6905:17: warning: ‘node’ may be used uninitialized in this function [-Wmaybe-uninitialized]
6905 | #pragma omp parallel for private(j,k,o,p,y_i,row) num_threads(nthreads)
| ^~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/include/Rdefines.h:38,
from ClusterML.c:11:
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:55:25: warning: ‘I’ may be used uninitialized in this function [-Wmaybe-uninitialized]
55 | #define Free(p) (R_chk_free( (void *)(p) ), (p) = NULL)
| ^~~~~~~~~~
ClusterML.c:6737:17: note: ‘I’ was declared here
6737 | double *I;
| ^
In file included from /home/biocbuild/bbs-3.17-bioc/R/include/Rdefines.h:38,
from ClusterML.c:11:
/home/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:55:25: warning: ‘Up’ may be used uninitialized in this function [-Wmaybe-uninitialized]
55 | #define Free(p) (R_chk_free( (void *)(p) ), (p) = NULL)
| ^~~~~~~~~~
ClusterML.c:6736:14: note: ‘Up’ was declared here
6736 | int *Up;
| ^~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c ClusterMP.c -o ClusterMP.o
ClusterMP.c: In function ‘clusterMP._omp_fn.0’:
ClusterMP.c:72:22: warning: ‘m’ may be used uninitialized in this function [-Wmaybe-uninitialized]
72 | int i, j, k, m, w;
| ^
ClusterMP.c:125:30: warning: ‘P’ may be used uninitialized in this function [-Wmaybe-uninitialized]
125 | int *P;
| ^
ClusterMP.c: In function ‘clusterMP’:
ClusterMP.c:540:17: warning: ‘Up’ may be used uninitialized in this function [-Wmaybe-uninitialized]
540 | free(Up);
| ^~~~~~~~
ClusterMP.c:113:17: warning: ‘subM’ may be used uninitialized in this function [-Wmaybe-uninitialized]
113 | #pragma omp parallel for private(i,j,k,m,w) num_threads(nthreads)
| ^~~
ClusterMP.c:113:17: warning: ‘nodes’ may be used uninitialized in this function [-Wmaybe-uninitialized]
ClusterMP.c:113:17: warning: ‘lengths’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c CommonGaps.c -o CommonGaps.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c Compositions.c -o Compositions.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c Compression.c -o Compression.o
Compression.c: In function ‘nbit._omp_fn.0’:
Compression.c:976:52: warning: ‘k’ may be used uninitialized in this function [-Wmaybe-uninitialized]
976 | p[c] = ((k - 1) >> 8) & 0xFF; // length of run
| ~~~^~~~
Compression.c:516:19: note: ‘k’ was declared here
516 | int i, j, k, pos;
| ^
Compression.c:1010:54: warning: ‘count’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1010 | count++;
| ~~~~~^~
Compression.c:542:43: note: ‘count’ was declared here
542 | unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
| ^~~~~
Compression.c:1009:62: warning: ‘word’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1009 | word = (word << 8) | (unsigned int)reorder(byte);
| ~~~~~~^~~~~
Compression.c:542:37: note: ‘word’ was declared here
542 | unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
| ^~~~
Compression.c:1212:56: warning: ‘rev’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1212 | p[c++] = rev==0 ? 254 : 255;
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~
Compression.c:543:41: note: ‘rev’ was declared here
543 | int lastTemp, currTemp, rev, len, len2, thresh = 1;
| ^~~
Compression.c:556:21: warning: ‘lower’ may be used uninitialized in this function [-Wmaybe-uninitialized]
556 | int lower = 0;
| ^~~~~
Compression.c:1239:71: warning: ‘lastTriplet’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1239 | if (threeBitEnd > threeBitBegin && (j - lastTriplet) > 20) {
| ~~~^~~~~~~~~~~~~~
Compression.c:629:26: note: ‘lastTriplet’ was declared here
629 | int run, lastTriplet, lastCase;
| ^~~~~~~~~~~
Compression.c:1029:79: warning: ‘dict’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1029 | lastHit = dict[(word >> k) & 0xFF];
| ^
Compression.c:542:31: note: ‘dict’ was declared here
542 | unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
| ^~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c ConsensusSequence.c -o ConsensusSequence.o
ConsensusSequence.c: In function ‘consensusProfile’:
ConsensusSequence.c:1578:17: warning: ‘DBN’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1578 | double *DBN, *s;
| ^~~
ConsensusSequence.c: In function ‘consensusProfileAA’:
ConsensusSequence.c:455:53: warning: ‘lastPos’ may be used uninitialized in this function [-Wmaybe-uninitialized]
455 | *(runs + s) += weight;
| ^~
ConsensusSequence.c:397:30: note: ‘lastPos’ was declared here
397 | int j, temp, length, lastPos, s = -1, value = -1, lastGap = start - 1;
| ^~~~~~~
ConsensusSequence.c:1771:17: warning: ‘HEC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1771 | double *HEC, *s;
| ^~~
ConsensusSequence.c: In function ‘colScores’:
ConsensusSequence.c:2040:48: warning: ‘curr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2040 | *(rans + k) += GO*(curr*total);
| ~~~~~^~~~~~~
ConsensusSequence.c:2040:48: warning: ‘total’ may be used uninitialized in this function [-Wmaybe-uninitialized]
ConsensusSequence.c:1939:27: warning: ‘d’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1939 | int do_DBN, n, l, d;
| ^
ConsensusSequence.c:1938:17: warning: ‘DBN’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1938 | double *DBN, *s;
| ^~~
ConsensusSequence.c: In function ‘colScoresAA’:
ConsensusSequence.c:2177:48: warning: ‘curr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2177 | *(rans + k) += GO*(curr*total);
| ~~~~~^~~~~~~
ConsensusSequence.c:2177:48: warning: ‘total’ may be used uninitialized in this function [-Wmaybe-uninitialized]
ConsensusSequence.c:2076:27: warning: ‘d’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2076 | int do_HEC, n, l, d;
| ^
ConsensusSequence.c:2075:17: warning: ‘HEC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2075 | double *HEC, *s;
| ^~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c ConsolidateGaps.c -o ConsolidateGaps.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -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:834:85: warning: ‘lastCycle’ may be used uninitialized in this function [-Wmaybe-uninitialized]
834 | cycles += lastCycle - thisCycle;
| ~~~~~~~~~~^~~~~~~~~~~
DesignProbes.c:267:58: note: ‘lastCycle’ was declared here
267 | int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles;
| ^~~~~~~~~
DesignProbes.c:834:85: warning: ‘thisCycle’ may be used uninitialized in this function [-Wmaybe-uninitialized]
834 | cycles += lastCycle - thisCycle;
| ~~~~~~~~~~^~~~~~~~~~~
DesignProbes.c:267:69: note: ‘thisCycle’ was declared here
267 | int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles;
| ^~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c Diff.c -o Diff.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c DistanceMatrix.c -o DistanceMatrix.o
DistanceMatrix.c: In function ‘firstSeqsPosEqual’:
DistanceMatrix.c:756:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
756 | if (!ci)
| ^~
DistanceMatrix.c:759:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
759 | while (i < ex) {
| ^~~~~
DistanceMatrix.c:778:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
778 | if (!cj)
| ^~
DistanceMatrix.c:781:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
781 | while (j < ey) {
| ^~~~~
DistanceMatrix.c: In function ‘similarities._omp_fn.0’:
DistanceMatrix.c:995:45: warning: ‘OV’ may be used uninitialized in this function [-Wmaybe-uninitialized]
995 | (double)(OV + g)/(double)w1 < coverage &&
| ~~~~^~~~
DistanceMatrix.c:843:45: note: ‘OV’ was declared here
843 | int i, j, n, s, p1, p2, t1, t2, ov, OV, g1, g2, g, o, count, *r;
| ^~
DistanceMatrix.c:1015:82: warning: ‘ov’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1015 | rans[i] = (double)s/((double)(ov + count + g2));
| ~~~^~~~~~~
DistanceMatrix.c:843:41: note: ‘ov’ was declared here
843 | int i, j, n, s, p1, p2, t1, t2, ov, OV, g1, g2, g, o, count, *r;
| ^~
DistanceMatrix.c:1000:44: warning: ‘o’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1000 | if (o == 1) {
| ^
DistanceMatrix.c:843:60: note: ‘o’ was declared here
843 | int i, j, n, s, p1, p2, t1, t2, ov, OV, g1, g2, g, o, count, *r;
| ^
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c EnumerateSequence.c -o EnumerateSequence.o
EnumerateSequence.c: In function ‘pop’:
EnumerateSequence.c:315:15: warning: suggest parentheses around ‘+’ in operand of ‘&’ [-Wparentheses]
315 | x = x + (x >> 4) & 0xF0F0F0F;
| ~~^~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c ExpandAmbiguities.c -o ExpandAmbiguities.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c FindFrameshifts.c -o FindFrameshifts.o
FindFrameshifts.c: In function ‘findFrameshifts’:
FindFrameshifts.c:381:35: warning: ‘K’ may be used uninitialized in this function [-Wmaybe-uninitialized]
381 | } else if (k==2) {
| ^
FindFrameshifts.c:318:47: warning: ‘J’ may be used uninitialized in this function [-Wmaybe-uninitialized]
318 | if (C[k*rc + j*r + i] >= 0) {
| ~^~
FindFrameshifts.c:370:43: warning: ‘I’ may be used uninitialized in this function [-Wmaybe-uninitialized]
370 | i += B[k*rc + j*r + i];
| ~~^~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/include/Rdefines.h:41,
from FindFrameshifts.c:11:
/home/biocbuild/bbs-3.17-bioc/R/include/Rinternals.h:893:33: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized]
893 | #define eval Rf_eval
| ^~~~~~~
FindFrameshifts.c:162:31: note: ‘utilsPackage’ was declared here
162 | SEXP percentComplete, utilsPackage;
| ^~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/include/Rdefines.h:41,
from FindFrameshifts.c:11:
/home/biocbuild/bbs-3.17-bioc/R/include/Rinternals.h:893:33: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
893 | #define eval Rf_eval
| ^~~~~~~
FindFrameshifts.c:162:14: note: ‘percentComplete’ was declared here
162 | SEXP percentComplete, utilsPackage;
| ^~~~~~~~~~~~~~~
FindFrameshifts.c:468:40: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
468 | before = *rPercentComplete;
| ~~~~~~~^~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c GeneFinding.c -o GeneFinding.o
GeneFinding.c: In function ‘scoreCodonModel’:
GeneFinding.c:422:59: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
422 | val += 4*getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c:432:64: warning: ‘lastVal’ may be used uninitialized in this function [-Wmaybe-uninitialized]
432 | score += codons[lastVal*64 + val];
| ~~~~~~~^~~
GeneFinding.c: In function ‘startCodonModel’:
GeneFinding.c:791:48: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
791 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c: In function ‘scoreStartCodonModel’:
GeneFinding.c:892:48: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
892 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c: In function ‘initialCodonModel’:
GeneFinding.c:973:59: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
973 | val += 4*getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c: In function ‘scoreInitialCodonModel’:
GeneFinding.c:1059:59: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1059 | val += 4*getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c: In function ‘terminationCodonModel’:
GeneFinding.c:1131:59: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1131 | val += 4*getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c: In function ‘scoreTerminationCodonModel’:
GeneFinding.c:1216:59: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1216 | val += 4*getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c: In function ‘getRegion’:
GeneFinding.c:1286:49: warning: ‘x_i.length’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1286 | (s==0 && j >= 0 && j + w <= x_i.length)) {
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
GeneFinding.c:1289:81: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1289 | seq[k] = getBaseLetterRC(x_i.ptr[j--]);
| ^
GeneFinding.c: In function ‘autocorrelationModel’:
GeneFinding.c:1379:59: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1379 | val += 4*getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c: In function ‘scoreAutocorrelationModel’:
GeneFinding.c:1496:59: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1496 | val += 4*getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c: In function ‘couplingModel’:
GeneFinding.c:1598:59: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1598 | val += 4*getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c: In function ‘scoreCouplingModel’:
GeneFinding.c:1712:59: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1712 | val += 4*getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c: In function ‘nucleotideBiasModel’:
GeneFinding.c:1826:56: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1826 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c: In function ‘scoreNucleotideBiasModel’:
GeneFinding.c:1913:56: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1913 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c: In function ‘upstreamMotifModel’:
GeneFinding.c:1990:77: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1990 | val += mult[k - 1]*getBaseRC(x_i.ptr[j + k - 1]);
| ^
GeneFinding.c: In function ‘scoreUpstreamMotifModel’:
GeneFinding.c:2090:77: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2090 | val += mult[k - 1]*getBaseRC(x_i.ptr[j + k - 1]);
| ^
GeneFinding.c: In function ‘scoreRunLengthModel’:
GeneFinding.c:2307:56: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2307 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c: In function ‘stopCodonModel’:
GeneFinding.c:2419:48: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2419 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c: In function ‘scoreStopCodonModel’:
GeneFinding.c:2520:48: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2520 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c: In function ‘codonFrequencies’:
GeneFinding.c:2578:59: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2578 | val += 4*getBaseRC(x_i.ptr[j++]);
| ^
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c GetPools.c -o GetPools.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c Import.c -o Import.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c InformationContent.c -o InformationContent.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c InsertGaps.c -o InsertGaps.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c IntDist.c -o IntDist.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -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:358:59: warning: ‘rans’ may be used uninitialized in this function [-Wmaybe-uninitialized]
358 | *(rans + k + l*s) += 1;
| ^~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c MovingAverage.c -o MovingAverage.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c MultiMatch.c -o MultiMatch.o
MultiMatch.c: In function ‘intMatchSelfOnce’:
MultiMatch.c:871:28: warning: variable ‘start’ set but not used [-Wunused-but-set-variable]
871 | int i, j, k, temp, start = 0;
| ^~~~~
MultiMatch.c: In function ‘matchOverlap._omp_fn.0’:
MultiMatch.c:1033:45: warning: ‘one’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1033 | two != one) {
| ~~~~^~~~~~
MultiMatch.c:1008:21: note: ‘one’ was declared here
1008 | int one, two;
| ^~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/include/Rdefines.h:41,
from MultiMatch.c:11:
MultiMatch.c: In function ‘matchLists’:
/home/biocbuild/bbs-3.17-bioc/R/include/Rinternals.h:893:33: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized]
893 | #define eval Rf_eval
| ^~~~~~~
MultiMatch.c:247:31: note: ‘utilsPackage’ was declared here
247 | SEXP percentComplete, utilsPackage;
| ^~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/include/Rdefines.h:41,
from MultiMatch.c:11:
/home/biocbuild/bbs-3.17-bioc/R/include/Rinternals.h:893:33: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
893 | #define eval Rf_eval
| ^~~~~~~
MultiMatch.c:247:14: note: ‘percentComplete’ was declared here
247 | SEXP percentComplete, utilsPackage;
| ^~~~~~~~~~~~~~~
MultiMatch.c:330:40: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
330 | before = *rPercentComplete;
| ~~~~~~~^~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c NNLS.c -o NNLS.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c Order.c -o Order.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c PairwiseAlignment.c -o PairwiseAlignment.o
PairwiseAlignment.c: In function ‘alignPair._omp_fn.0’:
PairwiseAlignment.c:469:39: warning: ‘p2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
469 | P2[i] = p2;
| ~~~~~~^~~~
PairwiseAlignment.c:173:19: note: ‘p2’ was declared here
173 | int *p1, *p2, *p3, *p4;
| ^~
PairwiseAlignment.c:468:39: warning: ‘p1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
468 | P1[i] = p1;
| ~~~~~~^~~~
PairwiseAlignment.c:173:14: note: ‘p1’ was declared here
173 | int *p1, *p2, *p3, *p4;
| ^~
PairwiseAlignment.c:473:39: warning: ‘p4’ may be used uninitialized in this function [-Wmaybe-uninitialized]
473 | P4[i] = p4;
| ~~~~~~^~~~
PairwiseAlignment.c:173:29: note: ‘p4’ was declared here
173 | int *p1, *p2, *p3, *p4;
| ^~
PairwiseAlignment.c:472:39: warning: ‘p3’ may be used uninitialized in this function [-Wmaybe-uninitialized]
472 | P3[i] = p3;
| ~~~~~~^~~~
PairwiseAlignment.c:173:24: note: ‘p3’ was declared here
173 | int *p1, *p2, *p3, *p4;
| ^~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c PredictDBN.c -o PredictDBN.o
PredictDBN.c: In function ‘predictDBN’:
PredictDBN.c:869:85: warning: ‘prev’ may be used uninitialized in this function [-Wmaybe-uninitialized]
869 | range2[0] = nucs[pos[prev]];// + 1;
| ^
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c PredictHEC.c -o PredictHEC.o
PredictHEC.c: In function ‘predictHEC’:
PredictHEC.c:255:25: warning: ‘ans’ may be used uninitialized in this function [-Wmaybe-uninitialized]
255 | SET_VECTOR_ELT(ret, i, ans);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
PredictHEC.c:233:51: warning: ‘states’ may be used uninitialized in this function [-Wmaybe-uninitialized]
233 | states[j] = 'C';
| ~~~~~~~~~~^~~~~
PredictHEC.c:237:46: warning: ‘rans’ may be used uninitialized in this function [-Wmaybe-uninitialized]
237 | *(rans + 3*j + 1) = E;
| ~~~~~~~~~~~~^~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c R_init_decipher.c -o R_init_decipher.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c RemoveGaps.c -o RemoveGaps.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c ReplaceChars.c -o ReplaceChars.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c SphericalKmeans.c -o SphericalKmeans.o
SphericalKmeans.c: In function ‘sphericalKmeans’:
SphericalKmeans.c:117:25: warning: ‘b’ may be used uninitialized in this function [-Wmaybe-uninitialized]
117 | free(b);
| ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c TerminalMismatch.c -o TerminalMismatch.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c Translate.c -o Translate.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c VectorSums.c -o VectorSums.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o DECIPHER.so AlignProfiles.o AssignIndels.o Biostrings_stubs.o CalculateDeltaG.o CalculateFISH.o ChainSegments.o Cluster.o ClusterML.o ClusterMP.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 PairwiseAlignment.o PredictDBN.o PredictHEC.o R_init_decipher.o RemoveGaps.o ReplaceChars.o S4Vectors_stubs.o SphericalKmeans.o TerminalMismatch.o Translate.o VectorSums.o XVector_stubs.o -fopenmp -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-DECIPHER/00new/DECIPHER/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** 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 | 0.055 | 0.012 | 0.067 | |
| Add2DB | 0.334 | 0.012 | 0.350 | |
| AdjustAlignment | 0.255 | 0.000 | 0.257 | |
| AlignDB | 1.271 | 0.060 | 1.334 | |
| AlignProfiles | 0.829 | 0.015 | 0.847 | |
| AlignSeqs | 26.742 | 0.424 | 27.173 | |
| AlignSynteny | 3.602 | 0.044 | 3.647 | |
| AlignTranslation | 14.792 | 0.108 | 14.904 | |
| AmplifyDNA | 0.004 | 0.000 | 0.006 | |
| Array2Matrix | 5.496 | 0.028 | 5.523 | |
| BrowseDB | 0.032 | 0.000 | 0.035 | |
| BrowseSeqs | 54.466 | 0.256 | 54.776 | |
| CalculateEfficiencyArray | 0.014 | 0.004 | 0.019 | |
| CalculateEfficiencyFISH | 0.006 | 0.000 | 0.005 | |
| CalculateEfficiencyPCR | 0.005 | 0.000 | 0.005 | |
| Clusterize | 7.778 | 0.052 | 7.833 | |
| Codec | 1.325 | 0.016 | 1.345 | |
| ConsensusSequence | 0.209 | 0.008 | 0.221 | |
| Cophenetic | 0.212 | 0.000 | 0.212 | |
| CorrectFrameshifts | 19.817 | 1.360 | 22.998 | |
| CreateChimeras | 0.962 | 0.004 | 0.967 | |
| DB2Seqs | 0.019 | 0.003 | 0.029 | |
| DesignArray | 5.062 | 0.044 | 5.108 | |
| DesignPrimers | 0.001 | 0.000 | 0.000 | |
| DesignProbes | 0.000 | 0.000 | 0.001 | |
| DesignSignatures | 0.001 | 0.000 | 0.001 | |
| DetectRepeats | 13.310 | 0.080 | 13.391 | |
| DigestDNA | 0.189 | 0.000 | 0.190 | |
| Disambiguate | 0.070 | 0.000 | 0.069 | |
| DistanceMatrix | 0.049 | 0.000 | 0.049 | |
| ExtractGenes | 50.771 | 0.388 | 51.168 | |
| FindChimeras | 0.082 | 0.004 | 0.096 | |
| FindGenes | 50.181 | 0.448 | 50.646 | |
| FindNonCoding | 99.552 | 14.212 | 136.762 | |
| FindSynteny | 1.841 | 0.037 | 1.894 | |
| FormGroups | 0.064 | 0.000 | 0.068 | |
| Genes-class | 49.319 | 9.163 | 71.853 | |
| HEC_MI | 0.231 | 0.012 | 0.259 | |
| IdConsensus | 0.954 | 8.603 | 22.053 | |
| IdLengths | 0.023 | 0.000 | 0.024 | |
| IdTaxa | 13.094 | 0.056 | 13.159 | |
| IdentifyByRank | 0.028 | 0.003 | 0.031 | |