Hi,  I cannot resolve the source of this error when I attempt to merge samples using phyloseq.  The command is:

> phymerge <- merge_samples(physeq, "expvar")

Error in `rownames<-`(`*tmp*`, value = c("PBRC_LR_BM4218", "PBRC_LR_BM4787",  : 

  attempt to set 'rownames' on an object with no dimensions

I downloaded the Global Patterns example and performed the command successfully with the example dataset.  Here is a snapshot of my data.

Thanks for taking a look,

Susan

> head(otu_table(physeq))

OTU Table:          [6 taxa and 4 samples]

                     taxa are rows

        PBRC_LR_BM4218 PBRC_LR_BM4787 PBRC_LR_BM8329 PBRC_LR_BM9418

OTU_43              61             10             10             18

OTU_65              11              5              6              3

OTU_110              6              0              0              1

OTU_85               0              0              0             13

OTU_15               5              1             11           1438

OTU_51              16              3              3             15

Taxonomy Table:     [6 taxa by 6 taxonomic ranks]:

        Domain     Phylum           Class                 Order             Family            

OTU_43  "Bacteria" "Actinobacteria" "Actinobacteria"      "Coriobacteridae" "Coriobacteriales"

OTU_65  "Bacteria" "Firmicutes"     "Bacilli"             "Lactobacillales" "Streptococcaceae"

OTU_110 "Bacteria" "Actinobacteria" "Actinobacteria"      "Coriobacteridae" "Coriobacteriales"

OTU_85  "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Caulobacterales" "Caulobacteraceae"

OTU_15  "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Pseudomonadales" "Moraxellaceae"   

OTU_51  "Bacteria" "Actinobacteria" "Actinobacteria"      "Coriobacteridae" "Coriobacteriales"

        Genus             

OTU_43  "Coriobacterineae"

OTU_65  "Streptococcus"   

OTU_110 "Coriobacterineae"

OTU_85  "Brevundimonas"   

OTU_15  "Acinetobacter"   

OTU_51  "Coriobacterineae"

head(sample_data(physeq))

Sample Data:        [4 samples by 1 sample variables]:

                               expvar

PBRC_LR_BM4218      A

PBRC_LR_BM4787      A

PBRC_LR_BM8329      B

PBRC_LR_BM9418      B

x<- as.data.frame(sample_data(physeq))

> str(x)

'data.frame':  4 obs. of  1 variable:

Formal class 'sample_data' [package "phyloseq"] with 4 slots

  ..@ .Data    :List of 1

  .. ..$ : Factor w/ 2 levels "A","B": 1 1 2 2

  ..@ names    : chr "expvar"

  ..@ row.names: chr  "PBRC_LR_BM4218" "PBRC_LR_BM4787" "PBRC_LR_BM8329" "PBRC_LR_BM9418"

  ..@ .S3Class : chr "data.frame"

sessionInfo()

R version 3.3.1 (2016-06-21)

Platform: x86_64-w64-mingw32/x64 (64-bit)

Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:

[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   

[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          

[5] LC_TIME=English_United States.1252    

attached base packages:

 [1] stats4    parallel  grid      stats     graphics  grDevices utils     datasets  methods  

[10] base     

other attached packages:

 [1] DESeq2_1.12.2              SummarizedExperiment_1.2.2 Biobase_2.32.0            

 [4] GenomicRanges_1.24.2       GenomeInfoDb_1.8.2         IRanges_2.6.0             

 [7] S4Vectors_0.10.1           BiocGenerics_0.18.0        shiny_0.13.2              

[10] vegan_2.4-0                lattice_0.20-33            permute_0.9-0             

[13] tidyr_0.5.1                doParallel_1.0.10          iterators_1.0.8           

[16] foreach_1.4.3              dplyr_0.5.0                plyr_1.8.4                

[19] scales_0.4.0               ggplot2_2.1.0              ape_3.5                   

[22] phyloseq_1.16.2           

loaded via a namespace (and not attached):

 [1] jsonlite_1.0         splines_3.3.1        Formula_1.2-1        assertthat_0.1      

 [5] latticeExtra_0.6-28  yaml_2.1.13          RSQLite_1.0.0        chron_2.3-47        

 [9] digest_0.6.9         RColorBrewer_1.1-2   XVector_0.12.0       colorspace_1.2-6    

[13] htmltools_0.3.5      httpuv_1.3.3         Matrix_1.2-6         XML_3.98-1.4        

[17] genefilter_1.54.2    zlibbioc_1.18.0      xtable_1.8-2         BiocParallel_1.6.2  

[21] tibble_1.1           annotate_1.50.0      mgcv_1.8-12          nnet_7.3-12         

[25] survival_2.39-4      magrittr_1.5         mime_0.5             nlme_3.1-128        

[29] MASS_7.3-45          foreign_0.8-66       tools_3.3.1          data.table_1.9.6    

[33] formatR_1.4          stringr_1.0.0        munsell_0.4.3        locfit_1.5-9.1      

[37] cluster_2.0.4        AnnotationDbi_1.34.3 Biostrings_2.40.1    ade4_1.7-4          

[41] rhdf5_2.16.0         biomformat_1.0.2     igraph_1.0.1         gtable_0.2.0        

[45] codetools_0.2-14     multtest_2.28.0      DBI_0.4-1            reshape2_1.4.1      

[49] R6_2.1.2             gridExtra_2.2.1      knitr_1.13           Hmisc_3.17-4        

[53] stringi_1.1.1        Rcpp_0.12.5          geneplotter_1.50.0   rpart_4.1-10        

[57] acepack_1.3-3.3