The error message occurs when reading one of the binary aroma data files, so it has nothing to do with writing per se. It basically says that the file header of the read file does not contain what it should. This indicates that the file is corrupt for one reason or the other.

I've updated aroma.core to report on the pathname as well when there's an error. Retry by installing:

source("http://callr.org/install#HenrikBengtsson/aroma.core@develop")

Have a look at the file reported. Is it's file size what you expect? If you extract the identifying file:

idx <- match(pathname, getPathname(dsTR))
df <- dsTR[[idx]]

and then try to inspect it:

print(df)

you should get the same error.

Next, try to exclude the file from the large set and recall writeDataFrame(), e.g.

dsTR2 <- dsTR[-idx]
writeDataFrame(dsTR2, ...)

from aroma.core.

Dear Henrik,
I have problems sourcing the file through our proxy, even though the "http_proxy" environment variable is set. Is there a way to source the file from local copy? I tried to source from a file but this failed.

source("http://callr.org/install#HenrikBengtsson/aroma.core@develop")
Installing/updating package: ‘aroma.core’
Error in gzfile(file, mode) : cannot open the connection
In addition: Warning message:
In gzfile(file, mode) :
cannot open compressed file '/scratch/tmp/RtmpPNmZwh/libloc_178_ccc298d560fce69b.rds', probable reason 'No such file or directory'

from aroma.core.

You could try to clone it to local directory and build from source;

git https://github.com/HenrikBengtsson/aroma.core.git
cd aroma.core
git checkout develop
cd ..
R CMD build aroma.core
R CMD INSTALL aroma.oore_3.0.0-9000.tar.gz

BTW, you probably want to run update.packages() first.

/H

UPDATE 2016-08-20: Incorrectly mentioned aroma.light above; now code is for aroma.core.

from aroma.core.

Dear Henrik,
Thank you, that worked with some tricks.
I will continue with the procedure you described in your earlier mail.
Thomas
Von: Henrik Bengtsson [mailto:[email protected]]
Gesendet: Freitag, 12. August 2016 13:25
An: HenrikBengtsson/aroma.core [email protected]
Cc: Thomas Grombacher [email protected]; Author [email protected]
Betreff: Re: [HenrikBengtsson/aroma.core] writing large logR data file as tab delimited txt file fails (#15)

You could try to clone it to local directory and build from source;

git https://github.com/HenrikBengtsson/aroma.light.git
cd aroma.light
git checkout develop
cd ..
R CMD build aroma.light
R CMD INSTALL aroma.light_3.0.0-9000.tar.gz

BTW, you probably want to run update.packages() first.

/H

On Fri, Aug 12, 2016 at 1:18 PM, ThomasGro <[email protected]mailto:[email protected]> wrote:

Dear Henrik,
I have problems sourcing the file through our proxy, even though the
"http_proxy" environment variable is set. Is there a way to source the file
from local copy? I tried to source from a file but this failed.

source("http://callr.org/install#HenrikBengtsson/aroma.core@develop")
Installing/updating package: ‘aroma.core’
Error in gzfile(file, mode) : cannot open the connection
In addition: Warning message:
In gzfile(file, mode) :
cannot open compressed file '/scratch/tmp/RtmpPNmZwh/
libloc_178_ccc298d560fce69b.rds', probable reason 'No such file or
directory'

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from aroma.core.

Dear Henrik,

I have tried to use your new getPathname() function, but this failed.
Please see the error message below:

sessionInfo()

R version 3.2.1 (2015-06-18)

Platform: x86_64-unknown-linux-gnu (64-bit)

locale:

[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C

[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8

[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8

[7] LC_PAPER=en_US.UTF-8 LC_NAME=C

[9] LC_ADDRESS=C LC_TELEPHONE=C

[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:

[1] stats graphics grDevices utils datasets methods base

other attached packages:

[1] aroma.light_3.3.1-9000 aroma.affymetrix_3.0.0 aroma.core_3.0.0

[4] R.devices_2.14.0 R.filesets_2.10.0 R.utils_2.3.0

[7] R.oo_1.20.0 affxparser_1.42.0 R.methodsS3_1.7.1

loaded via a namespace (and not attached):

[1] matrixStats_0.50.2 codetools_0.2-14 listenv_0.6.0 future_0.14.0

[5] digest_0.6.9 R.huge_0.9.0 PSCBS_0.61.0 tools_3.2.1

[9] R.cache_0.12.0 parallel_3.2.1 base64enc_0.1-3 aroma.apd_0.6.0

[13] R.rsp_0.30.0 globals_0.6.1 DNAcopy_1.44.0

getPathname(dsTR)

Error in UseMethod("getPathname") :

no applicable method for 'getPathname' applied to an object of class "c('AromaUnitTotalCnBinarySet', 'CopyNumberDataSet', 'AromaUnitSignalBinarySet', 'AromaTabularBinarySet', 'GenericTabularFileSet', 'GenericDataFileSet', 'FullNameInterface', 'Object')"

Any idea?

Best regards,
Thomas

Von: Henrik Bengtsson [mailto:[email protected]]
Gesendet: Freitag, 12. August 2016 12:25
An: HenrikBengtsson/aroma.core [email protected]
Cc: Thomas Grombacher [email protected]; Author [email protected]
Betreff: Re: [HenrikBengtsson/aroma.core] writing large logR data file as tab delimited txt file fails (#15)

from aroma.core.

My typo: it should be getPathnames(dsTR).

from aroma.core.

Thank you, Henrik.

Unfortunately the ‘pathname’ or ‘pathnames’ object is not generated by the command which leads to the error:
dsTRText<- writeDataFrame(dsTR, …)

And so the following statement fails

idx <- match(pathname, getPathname(dsTR))

Any ideas?

from aroma.core.

The update was not to fix the problem (because I don't know what it is), but to improve the error message so you / we can troubleshoot better; from #15 (comment):

"... to report on the pathname as well when there's an error ..."

So, run writeDataFrame() and look at the error message you get. With the new update you should now be able to see exactly which file is the problematic one. That is where the real troubleshooting starts.

from aroma.core.

I understand. But the error statement generated by writeDataFrame()is not changed to what I saw before:

sessionInfo()

R version 3.2.1 (2015-06-18)

Platform: x86_64-unknown-linux-gnu (64-bit)

locale:

[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C

[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8

[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8

[7] LC_PAPER=en_US.UTF-8 LC_NAME=C

[9] LC_ADDRESS=C LC_TELEPHONE=C

[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:

[1] stats graphics grDevices utils datasets methods base

other attached packages:

[1] aroma.light_3.3.1-9000 aroma.affymetrix_3.0.0 aroma.core_3.0.0

[4] R.devices_2.14.0 R.filesets_2.10.0 R.utils_2.3.0

[7] R.oo_1.20.0 affxparser_1.42.0 R.methodsS3_1.7.1

loaded via a namespace (and not attached):

[1] matrixStats_0.50.2 codetools_0.2-14 listenv_0.6.0 future_0.14.0

[5] digest_0.6.9 R.huge_0.9.0 PSCBS_0.61.0 tools_3.2.1

[9] R.cache_0.12.0 parallel_3.2.1 base64enc_0.1-3 aroma.apd_0.6.0

[13] R.rsp_0.30.0 globals_0.6.1 DNAcopy_1.44.0

writeDataFrame(dsTR, columns=c("unitName", "chromosome", "position", "*"))

[2016-08-18 12:46:24] Exception: File format error. The read "magic" does not match the existing one: [0x36,0x61,0x30,0x37,0x62] != [0x61,0x72,0x6f,0x6d,0x61]

at #12. readHeader.AromaTabularBinaryFile(this, con = con)

      - readHeader.AromaTabularBinaryFile() is in environment 'aroma.core'

at #11. readHeader(this, con = con)

      - readHeader() is in environment 'aroma.core'

at #10. readDataFrame.AromaTabularBinaryFile(this, rows = i, columns = j)

      - readDataFrame.AromaTabularBinaryFile() is in environment 'aroma.core'

at #9. NextMethod("readDataFrame", rows = rows)

      - NextMethod() is in environment 'base'

at #8. readDataFrame.AromaUnitSignalBinaryFile(this, rows = i, columns = j)

      - readDataFrame.AromaUnitSignalBinaryFile() is in environment 'aroma.core'

at #7. readDataFrame(this, rows = i, columns = j)

      - readDataFrame() is in environment 'R.filesets'

at #6. [.AromaTabularBinaryFile(df, unitsKK, , drop = FALSE)

      - `[.AromaTabularBinaryFile`() is in environment 'aroma.core'

at #5. df[unitsKK, , drop = FALSE]

      - NULL[]() is local of the calling function

at #4. writeDataFrame.AromaUnitSignalBinarySet(dsTR, columns = c("unitName",

          "chromosome", "position", "*"), filename = "ccle,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY,total.txt")

      - writeDataFrame.AromaUnitSignalBinarySet() is in environment 'aroma.core'

at #3. NextMethod("writeDataFrame", filename = filename)

      - NextMethod() is in environment 'base'

at #2. writeDataFrame.AromaUnitTotalCnBinarySet(dsTR, columns = c("unitName",

          "chromosome", "position", "*"))

      - writeDataFrame.AromaUnitTotalCnBinarySet() is in environment 'aroma.core'

at #1. writeDataFrame(dsTR, columns = c("unitName", "chromosome", "position",

          "*"))

      - writeDataFrame() is in environment 'R.utils'

Error: File format error. The read "magic" does not match the existing one: [0x36,0x61,0x30,0x37,0x62] != [0x61,0x72,0x6f,0x6d,0x61]

Von: Henrik Bengtsson [mailto:[email protected]]
Gesendet: Donnerstag, 18. August 2016 11:41
An: HenrikBengtsson/aroma.core [email protected]
Cc: Thomas Grombacher [email protected]; Author [email protected]
Betreff: Re: [HenrikBengtsson/aroma.core] writing large logR data file as tab delimited txt file fails (#15)

The update was not to fix the problem (because I don't know what it is), but to improve the error message so you / we can troubleshoot better; from #15 (comment)#15 (comment):

"... to report on the pathname as well when there's an error ..."

So, run writeDataFrame() and look at the error message you get. With the new update you should now be able to see exactly which file is the problematic one. That is where the real troubleshooting starts.

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from aroma.core.

Argh... my follow up instructions uaing Git mentioned aroma.light but should have been aroma.core. So retry with:

git https://github.com/HenrikBengtsson/aroma.core.git
cd aroma.core
git checkout develop
cd ..
R CMD build aroma.core
R CMD INSTALL aroma.core_3.0.0-9000.tar.gz

from aroma.core.

Still no there!?
The error statement generated by writeDataFrame()is not changed after using aroma.core_3.0.0-9000.
Any suggestion?

sessionInfo()

R version 3.2.1 (2015-06-18)

Platform: x86_64-unknown-linux-gnu (64-bit)

locale:

[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C

[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8

[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8

[7] LC_PAPER=en_US.UTF-8 LC_NAME=C

[9] LC_ADDRESS=C LC_TELEPHONE=C

[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:

[1] stats graphics grDevices utils datasets methods base

other attached packages:

[1] aroma.light_3.3.1-9000 aroma.affymetrix_3.0.0 aroma.core_3.0.0-9000

[4] R.devices_2.14.0 R.filesets_2.10.0 R.utils_2.3.0

[7] R.oo_1.20.0 affxparser_1.42.0 R.methodsS3_1.7.1

loaded via a namespace (and not attached):

[1] matrixStats_0.50.2 codetools_0.2-14 listenv_0.6.0 future_1.0.1

[5] digest_0.6.9 R.huge_0.9.0 PSCBS_0.61.0 tools_3.2.1

[9] R.cache_0.12.0 parallel_3.2.1 base64enc_0.1-3 aroma.apd_0.6.0

[13] R.rsp_0.30.0 globals_0.6.1 DNAcopy_1.44.0

writeDataFrame(dsTR, columns=c("unitName", "chromosome", "position", "*"))

[2016-08-18 14:10:28] Exception: File format error. The read "magic" does not match the existing one: [0x36,0x61,0x30,0x37,0x62] != [0x61,0x72,0x6f,0x6d,0x61]

at #12. readHeader.AromaTabularBinaryFile(this, con = con)

      - readHeader.AromaTabularBinaryFile() is in environment 'aroma.core'

at #11. readHeader(this, con = con)

      - readHeader() is in environment 'aroma.core'

at #10. readDataFrame.AromaTabularBinaryFile(this, rows = i, columns = j)

      - readDataFrame.AromaTabularBinaryFile() is in environment 'aroma.core'

at #9. NextMethod("readDataFrame", rows = rows)

      - NextMethod() is in environment 'base'

at #8. readDataFrame.AromaUnitSignalBinaryFile(this, rows = i, columns = j)

      - readDataFrame.AromaUnitSignalBinaryFile() is in environment 'aroma.core'

at #7. readDataFrame(this, rows = i, columns = j)

      - readDataFrame() is in environment 'R.filesets'

at #6. [.AromaTabularBinaryFile(df, unitsKK, , drop = FALSE)

      - `[.AromaTabularBinaryFile`() is in environment 'aroma.core'

at #5. df[unitsKK, , drop = FALSE]

      - NULL[]() is local of the calling function

at #4. writeDataFrame.AromaUnitSignalBinarySet(dsTR, columns = c("unitName",

          "chromosome", "position", "*"), filename = "ccle,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY,total.txt")

      - writeDataFrame.AromaUnitSignalBinarySet() is in environment 'aroma.core'

at #3. NextMethod("writeDataFrame", filename = filename)

      - NextMethod() is in environment 'base'

at #2. writeDataFrame.AromaUnitTotalCnBinarySet(dsTR, columns = c("unitName",

          "chromosome", "position", "*"))

      - writeDataFrame.AromaUnitTotalCnBinarySet() is in environment 'aroma.core'

at #1. writeDataFrame(dsTR, columns = c("unitName", "chromosome", "position",

          "*"))

      - writeDataFrame() is in environment 'R.utils'

Error: File format error. The read "magic" does not match the existing one: [0x36,0x61,0x30,0x37,0x62] != [0x61,0x72,0x6f,0x6d,0x61]

Von: Henrik Bengtsson [mailto:[email protected]]
Gesendet: Donnerstag, 18. August 2016 13:25
An: HenrikBengtsson/aroma.core [email protected]
Cc: Thomas Grombacher [email protected]; Author [email protected]
Betreff: Re: [HenrikBengtsson/aroma.core] writing large logR data file as tab delimited txt file fails (#15)

Argh... my follow up instructions uaing Git mentioned aroma.light but should have been aroma.core. So retry with:

git https://github.com/HenrikBengtsson/aroma.core.git

cd aroma.core

git checkout develop

cd ..

R CMD build aroma.core

R CMD INSTALL aroma.core_3.0.0-9000.tar.gz

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from aroma.core.

So, it should have been git clone ... not just git. Not sure if you figured that out yourself or not. Anyway, here is what I get when I try it on my computer and you should get the same:

mkdir tmp
cd tmp
git clone https://github.com/HenrikBengtsson/aroma.core.git
cd aroma.core
git checkout develop
git pull
R CMD build aroma.core
R CMD INSTALL aroma.core_3.0.0-9000.tar.gz

(I'm adding a git pull just in case you've already cloned an older version)

You should see something like:

$ git clone https://github.com/HenrikBengtsson/aroma.core.git

Cloning into 'aroma.core'...
remote: Counting objects: 6420, done.
remote: Compressing objects: 100% (1335/1335), done.
remote: Total 6420 (delta 5045), reused 6420 (delta 5045), pack-reused 0
Receiving objects: 100% (6420/6420), 1.61 MiB | 278.00 KiB/s, done.
Resolving deltas: 100% (5045/5045), done.
Checking connectivity... done.

$ cd aroma.core/
$ git checkout develop 
Branch develop set up to track remote branch develop from origin.
Switched to a new branch 'develop'

$ git pull
Already up-to-date.

$ cd ..

$ CMD build aroma.core
* checking for file ‘aroma.core/DESCRIPTION’ ... OK
* preparing ‘aroma.core’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building ‘aroma.core_3.0.0-9000.tar.gz’

$ R CMD INSTALL aroma.core_3.0.0-9000.tar.gz
* installing to library ‘/home/hb/R/x86_64-pc-linux-gnu-library/3.3’
* installing *source* package ‘aroma.core’ ...
** R
** inst
** preparing package for lazy loading
Warning in setGenericS3.default(name, export = exportGeneric, envir = envir,  :
  Renamed the preexisting function apply to apply.default, which was defined in environment base.
Warning in setGenericS3.default(name, export = exportGeneric, envir = envir,  :
  Renamed the preexisting function write to write.default, which was defined in environment base.
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (aroma.core)

To verify you've got the correct version installed, you should also see the following output in R:

> tail(head(aroma.core::readHeader.AromaTabularBinaryFile, 82), 10)
 [1]     trueMagic <- charToRaw("aroma")                                                                        
 [2]     magic <- readBin(con = con, what = raw(), n = length(trueMagic))                                       
 [3]     if (!identical(magic, trueMagic)) {                                                                    
 [4]         asStr <- function(raw) {                                                                           
 [5]             paste("[", paste(sprintf("%#0x", as.integer(raw)),                                             
 [6]                 collapse = ","), "]", sep = "")                                                            
 [7]         }                                                                                                  
 [8]         throw(sprintf("File format error. The read \\"magic\\" %s does not match the expected one %s: %s", 
 [9]             asStr(magic), asStr(trueMagic), pathnameT))                                                    
 [10]     }

That throw() statement is what generates the error message.

from aroma.core.

Yes, I did git clone and the installation from local package as you describe it. But as you might have anticipated, the package had not correctly been loaded in the running R session. So the code you added was not loaded.
I had to kill the session and start from a new session. After starting from a new session the new code worked and resulted in the following message:

Error: File format error. The read "magic" [0x36,0x61,0x30,0x37,0x62] does not match the expected one [0x61,0x72,0x6f,0x6d,0x61]: ‘rawCnData/ccle,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY/GenomeWideSNP_6/ARLES_p_NCLE_DNAAffy2_S_GenomeWideSNP_6_A01_256002,log2ratio,total.asb.md5’

I am a bit puzzled by the error message, though.
Does it mean that the “ARLES_p_NCLE_DNAAffy2_S_GenomeWideSNP_6_A01_256002,log2ratio,total.asb” file has not the correct MD5 checksum?
Or does it mean that the ARLES_p_NCLE_DNAAffy2_S_GenomeWideSNP_6_A01_256002,log2ratio,total.asb.md5” file is corrupt?

I checked both and the first seems to be correct!
According to what you suggested, I excluded the md5 file !?

Next, try to exclude the file for the large set and recall writeDataFrame(), e.g.

dsTR2 <- dsTR[-idx]

writeDataFrame(dsTR2, ...)

Then the next *.md5 file pops up as ‘File format error’.
Any idea why this could be the case?

Best,
Thomas

from aroma.core.

Aha... so, the *.asb.md5 files should not be inspected / validated, but only the *.asb files. In other words, there's something wrong (internally) that causes the dsTR object to also include the *.asb.md5 files. I'll try to identify and fix the bug next week. In the meanwhile, you can try:

keep <- grep("[.]asb$", getPathnames(dsTR))
dsTR <- dsTR[keep]

After this, dsTR should only contain *.asb files. Then retry writeDataFrame(dsTR).

(If this doesn't work for some reason, try to just remove the *.md5 files from the directory.)

from aroma.core.

I realized that I don't know how you create the dsTR object in the first place; what steps are you taking in order to create / get it?

from aroma.core.

I am running the pipeline which you have published at http://www.aroma-project.org/vignettes/CRMAv2/ on SNP6 tumor only samples using a Hapmap dataset as reference.
I did run the pipeline on several data sets already without having the current issues.

The code is below:

############################################################################################
#pipeline according to http://www.aroma-project.org/ including BAF improvement using CALMATE
############################################################################################
library('aroma.affymetrix')
verbose <- Arguments$getVerbose(-10, timestamp=TRUE)

Use 50 times more RAM than the default settings

setOption(aromaSettings, "memory/ram", 50.0)

######################
#annotation data files
######################
cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6",tag="Full")
csv <- AffymetrixNetAffxCsvFile$byChipType("GenomeWideSNP_6", pattern=".annot.csv$")

#define the data set to use here:
#############
#raw data set
#############
cs <- AffymetrixCelSet$byName("xxxx",chipType="GenomeWideSNP_6", cdf=cdf)
#here we define the hapmap reference set
csRef=AffymetrixCelSet$byName("hapmap_reference",chipType="GenomeWideSNP_6", cdf=cdf)

#####################################################
#Calibration for crosstalk between allele probe pairs
#####################################################
acc <- AllelicCrosstalkCalibration(cs, model="CRMAv2")
csC <- process(acc, verbose=verbose)
#############################################################
#Normalization for nucleotide-position probe sequence effects
#############################################################
bpn <- BasePositionNormalization(csC, target="zero")
csN <- process(bpn, verbose=verbose)

###############################################################################
#allele specific probe summarization for SNP6 using robust avarage and AvgCnPlm
###############################################################################
plm <- AvgCnPlm(csN, mergeStrands=TRUE, combineAlleles=FALSE)
if (length(findUnitsTodo(plm))>0){
units <- fitCnProbes(plm, verbose=verbose)
# Fit remaining units, i.e. SNPs (~5-10min/array)
units <- fit(plm, verbose=verbose)
}
ces <- getChipEffectSet(plm)
##############################################
#Normalization for PCR fragment-length effects
##############################################
fln <- FragmentLengthNormalization(ces, target="zero")
cesN <- process(fln, verbose=verbose)
#this is the AROMA result set!

###################################################
#CRMAv2/Export to technology-independent data files -- needed for use with CATLMATE
###################################################
dsNList <- exportTotalAndFracB(cesN, verbose=verbose);

##################################################################
##Generating total copy numbers relative to pool of hapmap samples
##################################################################
#this is not used since hapmap is used as reference:
##Calculating the robust average of all samples
##ceR <- getAverageFile(cesN, verbose=verbose)

#calculate the avarage of hapmap samples
ceR <- getAverageFile(csRef)

Calculate TCNs

dsTR <- exportTotalCnRatioSet(dsNList$total, refSet=ceR)

################################################
#write logR data files as tab delimited txt file
################################################
dsTRTxt<- writeDataFrame(dsTR, columns=c("unitName", "chromosome", "position", "*"))

###########################################
#using CALMATE to improve B-allele fraction
###########################################
library("calmate")
cmt <- CalMaTeCalibration(dsNList)
dsCList <- process(cmt, verbose=verbose)

#write calibrated B-fraction data to tab delimited file
dsCTxt<- writeDataFrame(dsCList$fracB, columns=c("unitName", "chromosome", "position", "*"))

Von: Henrik Bengtsson [mailto:[email protected]]
Gesendet: Montag, 22. August 2016 22:48
An: HenrikBengtsson/aroma.core [email protected]
Cc: Thomas Grombacher [email protected]; Author [email protected]
Betreff: Re: [HenrikBengtsson/aroma.core] writing large logR data file as tab delimited txt file fails (#15)

I realized that I don't know how you create the dsTR object in the first place; what steps are you taking in order to create / get it?

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I've fixed two bugs causing *.asb.md5 files to also be included in addition to *.asb files (see Issue #16) in the develop branch. Reinstall the updated develop branch (don't forget git pull since you're already cloned it). I believe it should be fixed now.

PS. I guess the reason why it "worked before" for you is that since aroma.* 3.0.0 (Jan 2016) several methods now generated *.md5 as well. Prior to 3.0.0 those were not generated and therefore the bug had no affect.

from aroma.core.

Great, thank you Henrik.
I will update my aroma package.
Thomas
Von: Henrik Bengtsson [mailto:[email protected]]
Gesendet: Donnerstag, 25. August 2016 19:51
An: HenrikBengtsson/aroma.core [email protected]
Cc: Thomas Grombacher [email protected]; Author [email protected]
Betreff: Re: [HenrikBengtsson/aroma.core] writing large logR data file as tab delimited txt file fails (#15)

I've fixed two bugs causing *.asb.md5 files to also be included in addition to *.asb files (see Issue #16#16) in the develop branch. Reinstall the updated develop branch (don't forget git pull since you're already cloned it). I believe it should be fixed now.

PS. I guess the reason why it "worked before" for you is that since aroma.* 3.0.0 (Jan 2016) several methods now generated *.md5 as well. Prior to 3.0.0 those were not generated and therefore the bug had no affect.

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from aroma.core.