[Bioc-devel] prebs failing in devel

Mon Apr 25 10:02:02 CEST 2016

Hi,

Now the problem with RPA package is fixed. However, PREBS fails to build on
Windows server because of a problem with GenomicRanges. GenomicRanges fails
to build on WindowsServer itself. Here is the error:

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf GenomicRanges.buildbin-libdir && mkdir
GenomicRanges.buildbin-libdir  && C:\cygwin\bin\curl.exe -O
http://zin2/BBS/3.3/bioc/src/contrib/GenomicRanges_1.23.27.tar.gz &&
E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build
--library=GenomicRanges.buildbin-libdir --merge-multiarch
GenomicRanges_1.23.27.tar.gz && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe
CMD INSTALL GenomicRanges_1.23.27.zip  && rm
GenomicRanges_1.23.27.tar.gz GenomicRanges_1.23.27.zip
###
##############################################################################
##############################################################################

install for i386

* installing *source* package 'GenomicRanges' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include"
-DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include"
-I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include"
-I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c
IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include"
-DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include"
-I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include"
-I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c
R_init_GenomicRanges.c -o R_init_GenomicRanges.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include"
-DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include"
-I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include"
-I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c
S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include"
-DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include"
-I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include"
-I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c
transcript_utils.c -o transcript_utils.o
transcript_utils.c: In function 'tlocs2rlocs':
transcript_utils.c:143:38: warning: 'end' may be used uninitialized in
this function [-Wmaybe-uninitialized]
  return on_minus_strand ? end - tloc : start + tloc;
                                      ^
transcript_utils.c:120:24: note: 'end' was declared here
  int nexons, j, start, end, width;
                        ^
transcript_utils.c:143:38: warning: 'start' may be used uninitialized
in this function [-Wmaybe-uninitialized]
  return on_minus_strand ? end - tloc : start + tloc;
                                      ^
transcript_utils.c:120:17: note: 'start' was declared here
  int nexons, j, start, end, width;
                 ^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o
GenomicRanges.dll tmp.def IRanges_stubs.o R_init_GenomicRanges.o
S4Vectors_stubs.o transcript_utils.o -Lc:/local323/lib/i386
-Lc:/local323/lib -LE:/biocbld/BBS-3˜1.3-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-3.3-bioc/meat/GenomicRanges.buildbin-libdir/GenomicRanges/libs/i386
** R
** inst
** preparing package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
  there is no package called 'zlibbioc'
ERROR: lazy loading failed for package 'GenomicRanges'
* removing 'E:/biocbld/bbs-3.3-bioc/meat/GenomicRanges.buildbin-libdir/GenomicRanges'
Warning: running command 'E:/biocbld/bbs-3.3-bioc/R/bin/i386/Rcmd.exe
INSTALL --library=GenomicRanges.buildbin-libdir
GenomicRanges_1.23.27.tar.gz --no-multiarch' had status 1

On Thu, Apr 21, 2016 at 5:40 PM, Karolis Uziela <
karolis.uziela at scilifelab.se> wrote:

> Regarding 2) I cant evalute more chunks, because they depend on packages
> that are not in Bioconductor (Custom CDF). Regarding 1) I will fix it
> On Apr 21, 2016 5:37 PM, "Karolis Uziela" <karolis.uziela at scilifelab.se>
> wrote:
>
>> The problem is that Leo Lahti has accidentally changed the output format
>> of his RPA package. I have already informed Leo regarding this and he
>> promised to fix it.
>> On Apr 21, 2016 5:16 PM, "Obenchain, Valerie" <
>> Valerie.Obenchain at roswellpark.org> wrote:
>>
>>> Karolis,
>>>
>>> prebs is failing on all platforms in devel:
>>>
>>> http://www.bioconductor.org/checkResults/devel/bioc-LATEST/
>>>
>>> I see there haven't been any recent commits so the problem may be with a
>>> dependency or change in R devel. I took a closer look at this pacakge
>>> and found these problems:
>>>
>>> 1) need to add library(prebsdata) to vignette
>>>
>>> 2) need to evaluation more vignette chunks
>>> Of 15 chunks only 4 are evaluated.
>>>
>>> 3) The vignette throws this error:
>>>
>>> > prebs_values <- calc_prebs(bam_files, manufacturer_cdf_mapping)
>>> Inferred name for CDF package: HGU133Plus2_mapping.txt -> hgu133plus2cdf
>>>
>>> [1] "Finished: input1.bam"
>>> [1] "Finished: input2.bam"
>>> Note: Some probe IDs contain duplicates. If you are using manufacturer's
>>> CDF then you can ignore this message.
>>>
>>> Estimated values for Bayesian prior:
>>>
>>> Alpha=1e-04
>>>
>>> Beta=0.0136640101662362
>>>
>>> Calculating Expression
>>> Error in (function (classes, fdef, mtable)  :
>>>   unable to find an inherited method for function ‘exprs’ for signature
>>> ‘"list"’
>>> In addition: Warning message:
>>> In rpa(abatch, bg.method = "none", cdf = CDF_NAME) :
>>>   RPA is a multi-array preprocessing method. The input affybatch has at
>>> most a single array, however. Returning expressionSet with no background
>>> correction or normalization.
>>> >
>>>
>>> Please have a look and check in a fix asap. We are freezing devel builds
>>> next week for the May 4 release. If the package isn't fixed by next
>>> Tuesday (26) we will start End of Life:
>>>
>>> http://www.bioconductor.org/developers/package-end-of-life/
>>>
>>> Let us know if you have questions.
>>>
>>> Valerie
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> This email message may contain legally privileged and/or confidential
>>> information.  If you are not the intended recipient(s), or the employee or
>>> agent responsible for the delivery of this message to the intended
>>> recipient(s), you are hereby notified that any disclosure, copying,
>>> distribution, or use of this email message is prohibited.  If you have
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>>>
>>

-- 

Karolis Uziela

PhD student
Science for Life Laboratory
Box 1031
17121 Solna, Sweden
Mob. +46 729 120 395

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