search for: xcms

Hi, I am using xcms library to read mass spectrum data. I generate objects from CDF files using the command line > SME10 <- xcmsRaw("SME_10.CDF") I have 50 CDF files with different name and I don't want to repeat the command for each one. Is there any option to read all the files and generate...

...is only " -Wall", while?CFLAGS are happy with "-g -O2 -Wall" This has an influence in at least one place https://stat.ethz.ch/pipermail/bioc-devel/2017-April/010733.html where we have WARNINGS in R CMD check from "Found ?abort?,? possibly from ?abort? (C)" in packages xcms/mzR. The abort() call is not coming from XCMS, but rather? from the C++ code in the STL: [...] # 1770 "/usr/include/c++/5/bits/stl_list.h" void _M_check_equal_allocators(list& __x) { ?if (_M_get_Node_allocator()) ???__builtin_abort(); } If we compile with -O2 optimisation, thi...

Hi everybody, I am a beginner in the steps of pre-processing and data analysis of non-targeted metabolomic profiling experiments. Anyone knows if there exists some tool for normalizing this type of data (raw data or XCMS matrix data) in R repositories? Many thanks in advance. Best regards, Núria ------------------------------------------------------- Núria Queralt Rosinach, Ph.D Bioinformatics technician Bioinformatics Unit IDIBAPS Edifici CEK C/ Rosselló, 153 08036 Barcelona TE: +34 93 227 54...

...printf XlcDL.c: reduce code duplication lcPubWrap: replace malloc(strlen) + strcpy with strdup Stop checking XTRANS_SECURE_RPC_FLAGS since we no longer use them Stop checking for preferred order of local transports Don't need to link libX11-xcb against libX11 xcms: use size_t for strlen/sizeof values instead of converting to int & back xcms: use unsigned indexes when looping through unsigned values xcms: use size_t for pointer offsets passed to strncmp Bhavi Dhingra (1): omGeneric.c: Correct the parameter usage of sizeof Christian Lin...

...ile?CFLAGS are happy with "-g -O2 > -Wall" > > This has an influence in at least one place > https://stat.ethz.ch/pipermail/bioc-devel/2017-April/010733.html > where we have WARNINGS in R CMD check from "Found ?abort?,? > possibly from ?abort? (C)" in packages xcms/mzR. > The abort() call is not coming from XCMS, but rather? > from the C++ code in the STL: > > [...] > # 1770 "/usr/include/c++/5/bits/stl_list.h" > void _M_check_equal_allocators(list& __x) { > ?if (_M_get_Node_allocator()) > ???__builtin_abort(); >...

.... I am trying to make a new object and it's not working. I get : Error in rematchDefinition(definition, fdef, mnames, fnames, signature) : methods can add arguments to the generic only if '...' is an argument to the generic as my error. I have included my code. It is from the xcms package. Any help would be great even if it's just telling me what the error means. I know that if I make "searchM" a normal function that it works but I would really like a method. Thank Paul require(methods) || stop("Couldn't load package methods") setClass("x...

I use R (2.15.2) on a windows 7 (64) for data mining with xcms package. This is a routine process for me and didn't encount any problems until few weeks ago when I got an error message for "R GUI frond end has stopped working". The following information was given by windows to describe the error. > \AppData\Local\Temp\WER5936.tmp.WERInte...

...wn Alan Coopersmith (23): Remove documentation of obsolete B16 & B32 tags in specs/libX11 Update README for gitlab migration Import reallocarray() from OpenBSD Convert main src directory to use reallocarray() Convert src/XKB to use reallocarray() Convert src/xcms to use reallocarray() Add some missing allocation failure checks in src/xcms Replace _XkbTypedRealloc & _XkbClearElems with new _XkbResizeArray Replace Xmalloc+strcpy pairs with strdup calls Convert src/xlibi18n to use reallocarray() Fix out-of-tree builds after co...

A package that I develop (xcms) sometimes needs to read and process vectors several hundreds of megabytes in size. (They only represent parts of a large data sets which can approach nearly 100GB.) Unfortunately, R sometimes hits the 2GB memory limit of Win32. To help cut the memory footprint in half, I'm implementing a &...

...mped the archive and wiki both. Adam Jackson (1): Bug #15884: Remove useless sleep()'s from the connection code. Alan Coopersmith (2): Fix mismatched brace indenting Update ac_define_dir macro in acinclude.m4 to 2008-04-12 version Bart Massey (1): added error check in Xcms color file parser; closes bug #15305 Christian Weisgerber (1): ConnDis: properly cast 'addr' before accessing it as a byte array. Colin Harrison (3): Fix typo Xlib warning fixes Fix missing error condition Daniel Stone (4): configure.ac: Don't search for...

...nt Spell out number in XkbGetKeyVirtualModMap man page to avoid cpp errors from # Add support for building lint library with --enable-lint-library Man page typo fixes Anton Zinoviev (1): Additions to the Compose file for UTF-8 Daniel Stone (1): Colours: Fix --disable-xcms Eric Anholt (2): Add XF86 keyboard/monitor brightness keysyms to the keysymbdb. Bug #2081: Note the range limitation of XSetScreenSaver arguments. Eric S. Raymond (9): Bug #9516: Markup error in XAllocWMHints.3x Bug 9523: Markup problems in XQueryExtension.3x Bug #96...

...y> <F> <U> : "<U+1F595>" U1F595 # REVERSED HAND WITH MIDDLE FINGER EXTENDED <Multi_key> <L> <L> <A> <P> : "<U+1F596>" U1F596 # RAISED HAND WITH PART BETWEEN MIDDLE AND RING FINGERS Alan Coopersmith (77): Xcms file parsing should not require the impossible to succeed Drop X_LOCALE fallback for OS'es without setlocale() unifdef -UISC XkbSelectEventDetails: remove unnecessary assignments _XkbReadGeomOverlay: check for NULL first, then use pointer Remove unused ETEST &...

Hi, I'm trying to match peaks between chromatographic runs. I'm able to match peaks when they are chromatographed with the same method, but not when there are different methods are used and spectra comes in to play. While searching I found the ALS package which should be usefull for my application, but I couldn't figure it out. I made some dummy chroms with R, which mimic my actual

...n "Re: Contents of R-help digest..." > > > Today's Topics: > > 1. Re: Combining two ANOVA outputs of different lengths > (Peter Dalgaard) > 2. Plot legend in margin (Daniel Brewer) > 3. Re : compute ROC curve? (justin bem) > 4. Re: reading xcms files (Prof Brian Ripley) > 5. Re: GLMM: MEEM error due to dichotomous variables > (lorenz.gygax@art.admin.ch) > 6. Re: Plot legend in margin (Daniel Brewer) > 7. Re: Plot legend in margin (Uwe Ligges) > 8. Re: Positioning text in top left corner of plot (Daniel Bre...