Hello Bernd and BioC people: Writing empty character strings results in a C-level HDF5 error starting in rhdf5 2.8.0. See transcript below, under 2.8.0 (I am not attaching the transcript under 2.7.3, where it works fine). I didn't test if this is specific to character or would happen with other types. I noticed in NEWS the note "h5createDataset automatically uses chunking and compression." in 2.8.0 so this may be related to that change. A workaround is to call h5createDataset and explicitly provide chunk = NULL (and level = 0 to suppress warning about compression requiring chunking). This should be done just before calling h5write. > library(rhdf5) > filename <- tempfile(fileext = ".hdf5") > datasetname <- "empty_char" > h5createFile(filename) [1] TRUE > h5write(character(0), + file = filename, + name = datasetname) HDF5-DIAG: Error detected in HDF5 (1.8.10) thread 0: #000: H5Pdcpl.c line 867 in H5Pset_chunk(): all chunk dimensions must be positive major: Invalid arguments to routine minor: Out of range HDF5-DIAG: Error detected in HDF5 (1.8.10) thread 0: #000: H5D.c line 170 in H5Dcreate2(): unable to create dataset major: Dataset minor: Unable to initialize object #001: H5Dint.c line 439 in H5D__create_named(): unable to create and link to dataset major: Dataset minor: Unable to initialize object #002: H5L.c line 1638 in H5L_link_object(): unable to create new link to object major: Links minor: Unable to initialize object #003: H5L.c line 1882 in H5L_create_real(): can't insert link major: Symbol table minor: Unable to insert object #004: H5Gtraverse.c line 861 in H5G_traverse(): internal path traversal failed major: Symbol table minor: Object not found #005: H5Gtraverse.c line 641 in H5G_traverse_real(): traversal operator failed major: Symbol table minor: Callback failed #006: H5L.c line 1685 in H5L_link_cb(): unable to create object major: Object header minor: Unable to initialize object #007: H5O.c line 3015 in H5O_obj_create(): unable to open object major: Object header minor: Can't open object #008: H5Doh.c line 293 in H5O__dset_create(): unable to create dataset major: Dataset minor: Unable to initialize object #009: H5Dint.c line 1001 in H5D__create(): filters can only be used with chunked layout major: Dataset minor: Bad value HDF5: unable to create dataset HDF5-DIAG: Error detected in HDF5 (1.8.10) thread 0: #000: H5D.c line 334 in H5Dopen2(): not found major: Dataset minor: Object not found #001: H5Gloc.c line 430 in H5G_loc_find(): can't find object major: Symbol table minor: Object not found #002: H5Gtraverse.c line 861 in H5G_traverse(): internal path traversal failed major: Symbol table minor: Object not found #003: H5Gtraverse.c line 641 in H5G_traverse_real(): traversal operator failed major: Symbol table minor: Callback failed #004: H5Gloc.c line 385 in H5G_loc_find_cb(): object 'empty_char' doesn't exist major: Symbol table minor: Object not found HDF5: unable to open dataset Error : Error in h5checktype(). Argument not of class H5IdComponent. In addition: Warning messages: 1: In max(nchar(obj)) : no non-missing arguments to max; returning -Inf 2: In H5Tset_size(tid, size) : NAs introduced by coercion Error : Error in h5checktype(). Argument not of class H5IdComponent. Error in is(h5id, "H5IdComponent") : object 'h5spaceFile' not found Error : Error in h5checktype(). Argument not of class H5IdComponent. > sessionInfo() R version 3.1.0 (2014-04-10) 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] rhdf5_2.8.0 loaded via a namespace (and not attached): [1] zlibbioc_1.10.0 [[alternative HTML version deleted]]

Dear Brad! It was a bug due to the automatic determination of chunk size introduced in rhdf5 2.8.0. I fixed the bug. It is again possible to write 0-length objects with h5write using rhdf 2.9.2 (available after the next daily bioconductor build). Best, Bernd On 11.06.2014, at 21:18, Brad Friedman <friedman.brad@gene.com> wrote: > Hello Bernd and BioC people: > > Writing empty character strings results in a C-level HDF5 error starting in rhdf5 2.8.0. See transcript below, under 2.8.0 (I am not attaching the transcript under 2.7.3, where it works fine). I didn't test if this is specific to character or would happen with other types. > > I noticed in NEWS the note "h5createDataset automatically uses chunking and compression." in 2.8.0 so this may be related to that change. > > A workaround is to call h5createDataset and explicitly provide chunk = NULL (and level = 0 to suppress warning about compression requiring chunking). This should be done just before calling h5write. > > > library(rhdf5) > > filename <- tempfile(fileext = ".hdf5") > > datasetname <- "empty_char" > > h5createFile(filename) > [1] TRUE > > h5write(character(0), > + file = filename, > + name = datasetname) > HDF5-DIAG: Error detected in HDF5 (1.8.10) thread 0: > #000: H5Pdcpl.c line 867 in H5Pset_chunk(): all chunk dimensions must be positive > major: Invalid arguments to routine > minor: Out of range > HDF5-DIAG: Error detected in HDF5 (1.8.10) thread 0: > #000: H5D.c line 170 in H5Dcreate2(): unable to create dataset > major: Dataset > minor: Unable to initialize object > #001: H5Dint.c line 439 in H5D__create_named(): unable to create and link to dataset > major: Dataset > minor: Unable to initialize object > #002: H5L.c line 1638 in H5L_link_object(): unable to create new link to object > major: Links > minor: Unable to initialize object > #003: H5L.c line 1882 in H5L_create_real(): can't insert link > major: Symbol table > minor: Unable to insert object > #004: H5Gtraverse.c line 861 in H5G_traverse(): internal path traversal failed > major: Symbol table > minor: Object not found > #005: H5Gtraverse.c line 641 in H5G_traverse_real(): traversal operator failed > major: Symbol table > minor: Callback failed > #006: H5L.c line 1685 in H5L_link_cb(): unable to create object > major: Object header > minor: Unable to initialize object > #007: H5O.c line 3015 in H5O_obj_create(): unable to open object > major: Object header > minor: Can't open object > #008: H5Doh.c line 293 in H5O__dset_create(): unable to create dataset > major: Dataset > minor: Unable to initialize object > #009: H5Dint.c line 1001 in H5D__create(): filters can only be used with chunked layout > major: Dataset > minor: Bad value > HDF5: unable to create dataset > HDF5-DIAG: Error detected in HDF5 (1.8.10) thread 0: > #000: H5D.c line 334 in H5Dopen2(): not found > major: Dataset > minor: Object not found > #001: H5Gloc.c line 430 in H5G_loc_find(): can't find object > major: Symbol table > minor: Object not found > #002: H5Gtraverse.c line 861 in H5G_traverse(): internal path traversal failed > major: Symbol table > minor: Object not found > #003: H5Gtraverse.c line 641 in H5G_traverse_real(): traversal operator failed > major: Symbol table > minor: Callback failed > #004: H5Gloc.c line 385 in H5G_loc_find_cb(): object 'empty_char' doesn't exist > major: Symbol table > minor: Object not found > HDF5: unable to open dataset > Error : Error in h5checktype(). Argument not of class H5IdComponent. > In addition: Warning messages: > 1: In max(nchar(obj)) : no non-missing arguments to max; returning -Inf > 2: In H5Tset_size(tid, size) : NAs introduced by coercion > Error : Error in h5checktype(). Argument not of class H5IdComponent. > Error in is(h5id, "H5IdComponent") : object 'h5spaceFile' not found > Error : Error in h5checktype(). Argument not of class H5IdComponent. > > sessionInfo() > R version 3.1.0 (2014-04-10) > 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] rhdf5_2.8.0 > > loaded via a namespace (and not attached): > [1] zlibbioc_1.10.0 > [[alternative HTML version deleted]]