Error in var(x) : is.atomic(y) is not TRUE

[Liviacmg]

I am trying to run this tutorial https://ycl6.github.io/16S-Demo/4_picrust2_tutorial.html and the following error occurs:

set.seed(123)
system.time({
aldex2_EC = aldex(p2EC, metadata$fecal_sample_type, mc.samples = 500, test = "t", effect = TRUE, denom = "iqlr", verbose = TRUE)
})
aldex.clr: generating Monte-Carlo instances and clr values
conditions vector supplied
operating in serial mode
removed rows with sums equal to zero
computing iqlr centering

Error in var(x) : is.atomic(y) is not TRUE
13.stop(simpleError(msg, call = if (p <- sys.parent(1L)) sys.call(p)))
12.stopifnot(is.atomic(y))
11.var(x)
10.var(x)
9.FUN(newX[, i], ...)
8.apply(reads.clr[these.rows, ], 2, function(x) {
var(x)
})
7.iqlr.features(reads, conds)
6.aldex.set.mode(reads, conds, denom)
5.aldex.clr.function(as.data.frame(reads), conds, mc.samples, denom,
verbose, useMC, summarizedExperiment = FALSE, gamma)
4.aldex.clr(reads = reads, conds = conditions, mc.samples = mc.samples,
denom = denom, verbose = verbose, useMC = FALSE, gamma = gamma)
3.aldex.clr(reads = reads, conds = conditions, mc.samples = mc.samples,
denom = denom, verbose = verbose, useMC = FALSE, gamma = gamma)
2.aldex(p2EC, metadata$fecal_sample_type, mc.samples = 500, test = "t",
effect = TRUE, denom = "iqlr", verbose = TRUE)
1.system.time({
aldex2_EC = aldex(p2EC, metadata$fecal_sample_type, mc.samples = 500,
test = "t", effect = TRUE, denom = "iqlr", verbose = TRUE)
})

Timing stopped at: 1.217 0.014 1.224

[ggloor]

Hmmm, this is usually a mismatch in input files.

can you provide a little bit more information on the format of the input files, and perhaps the first couple of lines?

[Liviacmg]

Hmmm, this is usually a mismatch in input files.

can you provide a little bit more information on the format of the input files, and perhaps the first couple of lines?

The input files are the picrust2 output files:

picrust2 = "/pathway/"

#Import PICRUSt2 results

p2_EC = paste0(picrust2, "/EC_metagenome_out/pred_metagenome_unstrat.tsv.gz")
p2_KO = paste0(picrust2, "/KO_metagenome_out/pred_metagenome_unstrat.tsv.gz")
p2_PW = paste0(picrust2, "/pathways_out/path_abun_unstrat.tsv.gz")

#Load picrust2 output files

p2EC = as.data.frame(fread(p2_EC))
rownames(p2EC) = p2EC$"function"
p2EC = as.matrix(p2EC[,-1])
p2EC = round(p2EC)

p2KO = as.data.frame(fread(p2_KO))
rownames(p2KO) = p2KO$"function"
p2KO = as.matrix(p2KO[,-1])
p2KO = round(p2KO)

p2PW = as.data.frame(fread(p2_PW))
rownames(p2PW) = p2PW$"pathway"
p2PW = as.matrix(p2PW[,-1])
p2PW = round(p2PW)

#Reading metadata file

metadata <- read_q2metadata("/pathway/sample-metadata-picrust.txt")
metadata <- metadata[order(metadata$SampleID),]
metadata$maternal_obesity,<- as.character(metadata$maternal_obesity,)

#EC

set.seed(123)
system.time({
aldex2_EC = aldex(p2EC, metadata$maternal_obesity, mc.samples = 500, test = "t", effect = TRUE, denom = "iqlr", verbose = TRUE)
})

#First lines of the files:

#p2EC:

SRR1556302 SRR1556810 SRR1556811 SRR1556812 SRR1556813 SRR1556814
EC:1.1.1.1 1045 6592 2477 2972 2065 2894
EC:1.1.1.100 1809 6671 5951 6826 4398 6364

#metadata

SampleID maternal_obesity
#q2:types categorical
SRR1556302 Obese
SRR1556810 Obese
SRR1556811 Non-Obese
SRR1556812 Non-Obese

Both input files have matching rows and columns:

ncol(p2EC)
[1] 79
nrow(metadata)
[1] 79

[Liviacmg]

When I run the script in my local machine it works, but when I try to run the exactly same scipt on a remote server it returns this error, even with different inputs.

[ggloor]

could you inspect the results of sessionInfo() from each machine after a clean start of the R session? my guess is that one of them has more recent R packages than the other.

[Liviacmg]

the sessionInfo() from the one that does not work:

R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.4 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C 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 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

time zone: America/Sao_Paulo
tzcode source: system (glibc)

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] cowplot_1.1.3 egg_0.4.5 gridExtra_2.3 qiime2R_0.99.6 lubridate_1.9.3
[6] forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4 purrr_1.0.2 readr_2.1.5
[11] tidyr_1.3.1 tibble_3.2.1 ggplot2_3.5.1 tidyverse_2.0.0 ALDEx2_1.36.0
[16] latticeExtra_0.6-30 lattice_0.22-6 zCompositions_1.5.0-4 truncnorm_1.0-9 NADA_1.6-1.1
[21] survival_3.7-0 MASS_7.3-61 phyloseq_1.48.0 data.table_1.16.0 R.utils_2.12.3
[26] R.oo_1.26.0 R.methodsS3_1.8.2

loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-3 rstudioapi_0.15.0 jsonlite_1.8.8
[4] magrittr_2.0.3 rmarkdown_2.25 zlibbioc_1.46.0
[7] vctrs_0.6.5 multtest_2.56.0 RCurl_1.98-1.14
[10] base64enc_0.1-3 htmltools_0.5.7 S4Arrays_1.4.1
[13] Rhdf5lib_1.22.1 SparseArray_1.4.8 Formula_1.2-5
[16] rhdf5_2.44.0 htmlwidgets_1.6.4 plyr_1.8.9
[19] igraph_2.0.1.1 lifecycle_1.0.4 iterators_1.0.14
[22] pkgconfig_2.0.3 Matrix_1.6-5 R6_2.5.1
[25] fastmap_1.1.1 GenomeInfoDbData_1.2.10 MatrixGenerics_1.16.0
[28] digest_0.6.34 colorspace_2.1-0 S4Vectors_0.38.2
[31] Hmisc_5.1-1 GenomicRanges_1.52.1 vegan_2.6-4
[34] RcppZiggurat_0.1.6 fansi_1.0.6 timechange_0.3.0
[37] abind_1.4-5 mgcv_1.9-1 compiler_4.4.1
[40] withr_3.0.0 htmlTable_2.4.2 backports_1.4.1
[43] BiocParallel_1.34.2 DelayedArray_0.30.1 biomformat_1.28.0
[46] permute_0.9-7 tools_4.4.1 foreign_0.8-86
[49] ape_5.7-1 nnet_7.3-19 glue_1.7.0
[52] quadprog_1.5-8 nlme_3.1-165 rhdf5filters_1.12.1
[55] grid_4.4.1 checkmate_2.3.1 cluster_2.1.6
[58] reshape2_1.4.4 ade4_1.7-22 generics_0.1.3
[61] gtable_0.3.5 tzdb_0.4.0 hms_1.1.3
[64] utf8_1.2.4 XVector_0.40.0 BiocGenerics_0.46.0
[67] foreach_1.5.2 pillar_1.9.0 splines_4.4.1
[70] deldir_2.0-4 directlabels_2024.1.21 tidyselect_1.2.0
[73] Biostrings_2.68.1 knitr_1.45 IRanges_2.34.1
[76] SummarizedExperiment_1.30.2 stats4_4.4.1 xfun_0.41
[79] Biobase_2.60.0 matrixStats_1.2.0 DT_0.31
[82] stringi_1.8.3 yaml_2.3.8 evaluate_0.23
[85] codetools_0.2-19 interp_1.1-6 cli_3.6.3
[88] RcppParallel_5.1.9 rpart_4.1.23 munsell_0.5.1
[91] Rcpp_1.0.12 GenomeInfoDb_1.36.4 png_0.1-7
[94] parallel_4.4.1 Rfast_2.1.0 jpeg_0.1-10
[97] bitops_1.0-7 scales_1.3.0 crayon_1.5.2
[100] rlang_1.1.4

the sessionInfo() from the one that works:

R version 4.4.1 (2024-06-14 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 22631)

Matrix products: default

locale:
[1] LC_COLLATE=Portuguese_Brazil.utf8 LC_CTYPE=Portuguese_Brazil.utf8
[3] LC_MONETARY=Portuguese_Brazil.utf8 LC_NUMERIC=C
[5] LC_TIME=Portuguese_Brazil.utf8

time zone: America/Sao_Paulo
tzcode source: internal

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] cowplot_1.1.3 egg_0.4.5 gridExtra_2.3 qiime2R_0.99.6
[5] lubridate_1.9.3 forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4
[9] purrr_1.0.2 readr_2.1.5 tidyr_1.3.1 tibble_3.2.1
[13] ggplot2_3.5.1 tidyverse_2.0.0 ALDEx2_1.36.0 latticeExtra_0.6-30
[17] lattice_0.22-6 zCompositions_1.5.0-4 truncnorm_1.0-9 NADA_1.6-1.1
[21] survival_3.6-4 MASS_7.3-60.2 data.table_1.16.0 phyloseq_1.48.0

loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-3 rstudioapi_0.16.0 jsonlite_1.8.8
[4] magrittr_2.0.3 rmarkdown_2.28 zlibbioc_1.50.0
[7] vctrs_0.6.5 multtest_2.60.0 base64enc_0.1-3
[10] htmltools_0.5.8.1 S4Arrays_1.4.1 Rhdf5lib_1.26.0
[13] SparseArray_1.4.8 Formula_1.2-5 rhdf5_2.48.0
[16] htmlwidgets_1.6.4 plyr_1.8.9 igraph_2.0.3
[19] lifecycle_1.0.4 iterators_1.0.14 pkgconfig_2.0.3
[22] Matrix_1.7-0 R6_2.5.1 fastmap_1.2.0
[25] GenomeInfoDbData_1.2.12 MatrixGenerics_1.16.0 digest_0.6.37
[28] colorspace_2.1-1 S4Vectors_0.42.1 Hmisc_5.1-3
[31] GenomicRanges_1.56.1 vegan_2.6-8 RcppZiggurat_0.1.6
[34] fansi_1.0.6 timechange_0.3.0 httr_1.4.7
[37] abind_1.4-8 mgcv_1.9-1 compiler_4.4.1
[40] withr_3.0.1 htmlTable_2.4.3 backports_1.5.0
[43] BiocParallel_1.38.0 DelayedArray_0.30.1 biomformat_1.32.0
[46] permute_0.9-7 tools_4.4.1 foreign_0.8-86
[49] ape_5.8 nnet_7.3-19 glue_1.7.0
[52] quadprog_1.5-8 nlme_3.1-164 rhdf5filters_1.16.0
[55] grid_4.4.1 checkmate_2.3.2 cluster_2.1.6
[58] reshape2_1.4.4 ade4_1.7-22 generics_0.1.3
[61] gtable_0.3.5 tzdb_0.4.0 hms_1.1.3
[64] utf8_1.2.4 XVector_0.44.0 BiocGenerics_0.50.0
[67] foreach_1.5.2 pillar_1.9.0 splines_4.4.1
[70] deldir_2.0-4 directlabels_2024.1.21 tidyselect_1.2.1
[73] Biostrings_2.72.1 knitr_1.48 IRanges_2.38.1
[76] SummarizedExperiment_1.34.0 stats4_4.4.1 xfun_0.47
[79] Biobase_2.64.0 matrixStats_1.4.1 DT_0.33
[82] stringi_1.8.4 UCSC.utils_1.0.0 yaml_2.3.10
[85] evaluate_1.0.0 codetools_0.2-20 interp_1.1-6
[88] BiocManager_1.30.25 cli_3.6.3 RcppParallel_5.1.9
[91] rpart_4.1.23 munsell_0.5.1 Rcpp_1.0.13
[94] GenomeInfoDb_1.40.1 png_0.1-8 parallel_4.4.1
[97] Rfast_2.1.0 jpeg_0.1-10 scales_1.3.0
[100] crayon_1.5.3 rlang_1.1.4