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This page was generated on 2025-11-13 15:41 -0500 (Thu, 13 Nov 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4903
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Package 383/435HostnameOS / ArchINSTALLBUILDCHECK
spatialLIBD 1.22.0  (landing page)
Leonardo Collado-Torres
Snapshot Date: 2025-11-13 07:30 -0500 (Thu, 13 Nov 2025)
git_url: https://git.bioconductor.org/packages/spatialLIBD
git_branch: RELEASE_3_22
git_last_commit: d06d43c
git_last_commit_date: 2025-10-29 10:02:34 -0500 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published


CHECK results for spatialLIBD on nebbiolo2

To the developers/maintainers of the spatialLIBD package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: spatialLIBD
Version: 1.22.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:spatialLIBD.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings spatialLIBD_1.22.0.tar.gz
StartedAt: 2025-11-13 13:12:09 -0500 (Thu, 13 Nov 2025)
EndedAt: 2025-11-13 13:32:27 -0500 (Thu, 13 Nov 2025)
EllapsedTime: 1218.3 seconds
RetCode: 0
Status:   OK  
CheckDir: spatialLIBD.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:spatialLIBD.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings spatialLIBD_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-data-experiment/meat/spatialLIBD.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘spatialLIBD/DESCRIPTION’ ... OK
* this is package ‘spatialLIBD’ version ‘1.22.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 36 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘spatialLIBD’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  check_sce.Rd: SingleCellExperiment-class
  check_sce_layer.Rd: SingleCellExperiment-class
  fetch_data.Rd: SingleCellExperiment-class
  layer_boxplot.Rd: SingleCellExperiment-class
  run_app.Rd: SingleCellExperiment-class
  sce_to_spe.Rd: SingleCellExperiment-class
  sig_genes_extract.Rd: SingleCellExperiment-class
  sig_genes_extract_all.Rd: SingleCellExperiment-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
vis_gene                 28.452  2.239  31.606
vis_clus                 21.610  2.344  24.824
add_images               20.675  3.077  26.188
img_update_all           18.884  1.350  20.711
add_qc_metrics           16.846  1.713  18.813
vis_image                16.673  1.738  20.261
vis_grid_gene            16.355  1.717  19.301
vis_grid_clus            16.088  1.954  20.197
cluster_export           15.982  1.910  18.587
cluster_import           16.143  1.559  18.868
vis_clus_p               16.134  1.411  20.115
add_key                  15.942  1.534  19.047
vis_gene_p               14.795  1.162  17.078
img_edit                 14.449  1.415  16.649
img_update               14.396  1.418  16.825
frame_limits             14.220  1.546  16.860
geom_spatial             14.528  1.228  17.602
check_spe                14.186  1.187  16.172
sce_to_spe               14.037  1.285  19.595
gene_set_enrichment_plot  7.802  0.453   8.697
layer_stat_cor_plot       4.180  0.338   5.201
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-data-experiment/meat/spatialLIBD.Rcheck/00check.log’
for details.


Installation output

spatialLIBD.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL spatialLIBD
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘spatialLIBD’ ...
** this is package ‘spatialLIBD’ version ‘1.22.0’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (spatialLIBD)

Tests output

spatialLIBD.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(spatialLIBD)
Loading required package: SpatialExperiment
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: Seqinfo
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

> 
> test_check("spatialLIBD")

rgstr_> ## Ensure reproducibility of example data
rgstr_> set.seed(20220907)

rgstr_> ## Generate example data
rgstr_> sce <- scuttle::mockSCE()

rgstr_> ## Add some sample IDs
rgstr_> sce$sample_id <- sample(LETTERS[1:5], ncol(sce), replace = TRUE)

rgstr_> ## Add a sample-level covariate: age
rgstr_> ages <- rnorm(5, mean = 20, sd = 4)

rgstr_> names(ages) <- LETTERS[1:5]

rgstr_> sce$age <- ages[sce$sample_id]

rgstr_> ## Add gene-level information
rgstr_> rowData(sce)$gene_id <- paste0("ENSG", seq_len(nrow(sce)))

rgstr_> rowData(sce)$gene_name <- paste0("gene", seq_len(nrow(sce)))

rgstr_> ## Pseudo-bulk by Cell Cycle
rgstr_> sce_pseudo <- registration_pseudobulk(
rgstr_+     sce,
rgstr_+     var_registration = "Cell_Cycle",
rgstr_+     var_sample_id = "sample_id",
rgstr_+     covars = c("age"),
rgstr_+     min_ncells = NULL
rgstr_+ )

rgstr_> colData(sce_pseudo)
DataFrame with 20 rows and 9 columns
     Mutation_Status  Cell_Cycle   Treatment   sample_id       age
         <character> <character> <character> <character> <numeric>
A_G0              NA          G0          NA           A   19.1872
B_G0              NA          G0          NA           B   25.3496
C_G0              NA          G0          NA           C   24.1802
D_G0              NA          G0          NA           D   15.5211
E_G0              NA          G0          NA           E   20.9701
...              ...         ...         ...         ...       ...
A_S               NA           S          NA           A   19.1872
B_S               NA           S          NA           B   25.3496
C_S               NA           S          NA           C   24.1802
D_S               NA           S          NA           D   15.5211
E_S               NA           S          NA           E   20.9701
     registration_variable registration_sample_id    ncells pseudo_sum_umi
               <character>            <character> <integer>      <numeric>
A_G0                    G0                      A         8        2946915
B_G0                    G0                      B        13        4922867
C_G0                    G0                      C         9        3398888
D_G0                    G0                      D         7        2630651
E_G0                    G0                      E        10        3761710
...                    ...                    ...       ...            ...
A_S                      S                      A        12        4516334
B_S                      S                      B         8        2960685
C_S                      S                      C         7        2595774
D_S                      S                      D        14        5233560
E_S                      S                      E        11        4151818

rgstr_> rowData(sce_pseudo)
DataFrame with 2000 rows and 3 columns
              gene_id   gene_name        gene_search
          <character> <character>        <character>
Gene_0001       ENSG1       gene1       gene1; ENSG1
Gene_0002       ENSG2       gene2       gene2; ENSG2
Gene_0003       ENSG3       gene3       gene3; ENSG3
Gene_0004       ENSG4       gene4       gene4; ENSG4
Gene_0005       ENSG5       gene5       gene5; ENSG5
...               ...         ...                ...
Gene_1996    ENSG1996    gene1996 gene1996; ENSG1996
Gene_1997    ENSG1997    gene1997 gene1997; ENSG1997
Gene_1998    ENSG1998    gene1998 gene1998; ENSG1998
Gene_1999    ENSG1999    gene1999 gene1999; ENSG1999
Gene_2000    ENSG2000    gene2000 gene2000; ENSG2000

rgstr_> ## Ensure reproducibility of example data
rgstr_> set.seed(20220907)

rgstr_> ## Generate example data
rgstr_> sce <- scuttle::mockSCE()

rgstr_> ## Add some sample IDs
rgstr_> sce$sample_id <- sample(LETTERS[1:5], ncol(sce), replace = TRUE)

rgstr_> ## Add a sample-level covariate: age
rgstr_> ages <- rnorm(5, mean = 20, sd = 4)

rgstr_> names(ages) <- LETTERS[1:5]

rgstr_> sce$age <- ages[sce$sample_id]

rgstr_> ## Add gene-level information
rgstr_> rowData(sce)$gene_id <- paste0("ENSG", seq_len(nrow(sce)))

rgstr_> rowData(sce)$gene_name <- paste0("gene", seq_len(nrow(sce)))

rgstr_> ## Pseudo-bulk by Cell Cycle
rgstr_> sce_pseudo <- registration_pseudobulk(
rgstr_+     sce,
rgstr_+     var_registration = "Cell_Cycle",
rgstr_+     var_sample_id = "sample_id",
rgstr_+     covars = c("age"),
rgstr_+     min_ncells = NULL
rgstr_+ )

rgstr_> colData(sce_pseudo)
DataFrame with 20 rows and 9 columns
     Mutation_Status  Cell_Cycle   Treatment   sample_id       age
         <character> <character> <character> <character> <numeric>
A_G0              NA          G0          NA           A   19.1872
B_G0              NA          G0          NA           B   25.3496
C_G0              NA          G0          NA           C   24.1802
D_G0              NA          G0          NA           D   15.5211
E_G0              NA          G0          NA           E   20.9701
...              ...         ...         ...         ...       ...
A_S               NA           S          NA           A   19.1872
B_S               NA           S          NA           B   25.3496
C_S               NA           S          NA           C   24.1802
D_S               NA           S          NA           D   15.5211
E_S               NA           S          NA           E   20.9701
     registration_variable registration_sample_id    ncells pseudo_sum_umi
               <character>            <character> <integer>      <numeric>
A_G0                    G0                      A         8        2946915
B_G0                    G0                      B        13        4922867
C_G0                    G0                      C         9        3398888
D_G0                    G0                      D         7        2630651
E_G0                    G0                      E        10        3761710
...                    ...                    ...       ...            ...
A_S                      S                      A        12        4516334
B_S                      S                      B         8        2960685
C_S                      S                      C         7        2595774
D_S                      S                      D        14        5233560
E_S                      S                      E        11        4151818

rgstr_> rowData(sce_pseudo)
DataFrame with 2000 rows and 3 columns
              gene_id   gene_name        gene_search
          <character> <character>        <character>
Gene_0001       ENSG1       gene1       gene1; ENSG1
Gene_0002       ENSG2       gene2       gene2; ENSG2
Gene_0003       ENSG3       gene3       gene3; ENSG3
Gene_0004       ENSG4       gene4       gene4; ENSG4
Gene_0005       ENSG5       gene5       gene5; ENSG5
...               ...         ...                ...
Gene_1996    ENSG1996    gene1996 gene1996; ENSG1996
Gene_1997    ENSG1997    gene1997 gene1997; ENSG1997
Gene_1998    ENSG1998    gene1998 gene1998; ENSG1998
Gene_1999    ENSG1999    gene1999 gene1999; ENSG1999
Gene_2000    ENSG2000    gene2000 gene2000; ENSG2000

rgst__> example("registration_model", package = "spatialLIBD")

rgstr_> example("registration_pseudobulk", package = "spatialLIBD")

rgstr_> ## Ensure reproducibility of example data
rgstr_> set.seed(20220907)

rgstr_> ## Generate example data
rgstr_> sce <- scuttle::mockSCE()

rgstr_> ## Add some sample IDs
rgstr_> sce$sample_id <- sample(LETTERS[1:5], ncol(sce), replace = TRUE)

rgstr_> ## Add a sample-level covariate: age
rgstr_> ages <- rnorm(5, mean = 20, sd = 4)

rgstr_> names(ages) <- LETTERS[1:5]

rgstr_> sce$age <- ages[sce$sample_id]

rgstr_> ## Add gene-level information
rgstr_> rowData(sce)$gene_id <- paste0("ENSG", seq_len(nrow(sce)))

rgstr_> rowData(sce)$gene_name <- paste0("gene", seq_len(nrow(sce)))

rgstr_> ## Pseudo-bulk by Cell Cycle
rgstr_> sce_pseudo <- registration_pseudobulk(
rgstr_+     sce,
rgstr_+     var_registration = "Cell_Cycle",
rgstr_+     var_sample_id = "sample_id",
rgstr_+     covars = c("age"),
rgstr_+     min_ncells = NULL
rgstr_+ )

rgstr_> colData(sce_pseudo)
DataFrame with 20 rows and 9 columns
     Mutation_Status  Cell_Cycle   Treatment   sample_id       age
         <character> <character> <character> <character> <numeric>
A_G0              NA          G0          NA           A   19.1872
B_G0              NA          G0          NA           B   25.3496
C_G0              NA          G0          NA           C   24.1802
D_G0              NA          G0          NA           D   15.5211
E_G0              NA          G0          NA           E   20.9701
...              ...         ...         ...         ...       ...
A_S               NA           S          NA           A   19.1872
B_S               NA           S          NA           B   25.3496
C_S               NA           S          NA           C   24.1802
D_S               NA           S          NA           D   15.5211
E_S               NA           S          NA           E   20.9701
     registration_variable registration_sample_id    ncells pseudo_sum_umi
               <character>            <character> <integer>      <numeric>
A_G0                    G0                      A         8        2946915
B_G0                    G0                      B        13        4922867
C_G0                    G0                      C         9        3398888
D_G0                    G0                      D         7        2630651
E_G0                    G0                      E        10        3761710
...                    ...                    ...       ...            ...
A_S                      S                      A        12        4516334
B_S                      S                      B         8        2960685
C_S                      S                      C         7        2595774
D_S                      S                      D        14        5233560
E_S                      S                      E        11        4151818

rgstr_> rowData(sce_pseudo)
DataFrame with 2000 rows and 3 columns
              gene_id   gene_name        gene_search
          <character> <character>        <character>
Gene_0001       ENSG1       gene1       gene1; ENSG1
Gene_0002       ENSG2       gene2       gene2; ENSG2
Gene_0003       ENSG3       gene3       gene3; ENSG3
Gene_0004       ENSG4       gene4       gene4; ENSG4
Gene_0005       ENSG5       gene5       gene5; ENSG5
...               ...         ...                ...
Gene_1996    ENSG1996    gene1996 gene1996; ENSG1996
Gene_1997    ENSG1997    gene1997 gene1997; ENSG1997
Gene_1998    ENSG1998    gene1998 gene1998; ENSG1998
Gene_1999    ENSG1999    gene1999 gene1999; ENSG1999
Gene_2000    ENSG2000    gene2000 gene2000; ENSG2000

rgstr_> registration_mod <- registration_model(sce_pseudo, "age")

rgstr_> head(registration_mod)
     registration_variableG0 registration_variableG1 registration_variableG2M
A_G0                       1                       0                        0
B_G0                       1                       0                        0
C_G0                       1                       0                        0
D_G0                       1                       0                        0
E_G0                       1                       0                        0
A_G1                       0                       1                        0
     registration_variableS      age
A_G0                      0 19.18719
B_G0                      0 25.34965
C_G0                      0 24.18019
D_G0                      0 15.52107
E_G0                      0 20.97006
A_G1                      0 19.18719

rgst__> block_cor <- registration_block_cor(sce_pseudo, registration_mod)
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 47 ]
> 
> proc.time()
   user  system elapsed 
111.431   7.346 127.486 

Example timings

spatialLIBD.Rcheck/spatialLIBD-Ex.timings

nameusersystemelapsed
add10xVisiumAnalysis000
add_images20.675 3.07726.188
add_key15.942 1.53419.047
add_qc_metrics16.846 1.71318.813
annotate_registered_clusters1.1340.0821.470
check_modeling_results1.1210.0341.398
check_sce3.3330.1083.652
check_sce_layer1.4230.1281.753
check_spe14.186 1.18716.172
cluster_export15.982 1.91018.587
cluster_import16.143 1.55918.868
enough_ram0.0030.0070.010
fetch_data1.2210.0821.542
frame_limits14.220 1.54616.860
gene_set_enrichment1.2100.0631.521
gene_set_enrichment_plot7.8020.4538.697
geom_spatial14.528 1.22817.602
get_colors1.2210.0421.539
img_edit14.449 1.41516.649
img_update14.396 1.41816.825
img_update_all18.884 1.35020.711
layer_boxplot3.0780.0813.682
layer_stat_cor1.2190.0431.460
layer_stat_cor_plot4.1800.3385.201
locate_images000
read10xVisiumAnalysis000
read10xVisiumWrapper0.0010.0000.000
registration_block_cor2.7520.0462.799
registration_model0.7310.0020.734
registration_pseudobulk0.6220.0020.624
registration_stats_anova2.8240.0302.855
registration_stats_enrichment2.9540.0202.974
registration_stats_pairwise2.7910.0242.815
registration_wrapper4.2500.0054.255
run_app0.0010.0000.000
sce_to_spe14.037 1.28519.595
sig_genes_extract2.5390.1373.131
sig_genes_extract_all3.1060.0703.609
sort_clusters0.0080.0000.007
vis_clus21.610 2.34424.824
vis_clus_p16.134 1.41120.115
vis_gene28.452 2.23931.606
vis_gene_p14.795 1.16217.078
vis_grid_clus16.088 1.95420.197
vis_grid_gene16.355 1.71719.301
vis_image16.673 1.73820.261