Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R [S] T  U  V  W  X  Y  Z 

BioC 3.0: CHECK report for STRINGdb on oaxaca

This page was generated on 2015-04-10 10:08:01 -0700 (Fri, 10 Apr 2015).

Package 871/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
STRINGdb 1.5.5
Andrea Franceschini , Alexander Roth , Christian Von Mering , Michael Kuhn , Lars J Jensen
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/STRINGdb
Last Changed Rev: 98967 / Revision: 102249
Last Changed Date: 2015-02-02 10:07:39 -0800 (Mon, 02 Feb 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ ERROR ] OK 

Summary

Package: STRINGdb
Version: 1.5.5
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch STRINGdb_1.5.5.tar.gz
StartedAt: 2015-04-10 03:45:00 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 03:53:11 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 491.2 seconds
RetCode: 1
Status:  ERROR 
CheckDir: STRINGdb.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch STRINGdb_1.5.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/STRINGdb.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘STRINGdb/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘STRINGdb’ version ‘1.5.5’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘png’ ‘sqldf’ ‘plyr’ ‘igraph’ ‘RCurl’ ‘plotrix’ ‘RColorBrewer’
  ‘gplots’ ‘hash’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘STRINGdb’ can be installed ... [6s/6s] OK
* checking installed package size ... NOTE
  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
* 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 R 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘RColorBrewer’ ‘RCurl’ ‘gplots’ ‘hash’ ‘igraph’ ‘methods’ ‘plotrix’
  ‘plyr’ ‘png’ ‘sqldf’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
get_STRING_species: no visible binding for global variable
  ‘official_name’
postFormSmart: no visible global function definition for ‘curlOptions’
postFormSmart: no visible global function definition for
  ‘getCurlHandle’
postFormSmart: no visible binding for global variable ‘curlEscape’
postFormSmart: no visible global function definition for ‘postForm’
ppi_enrichment: no visible global function definition for ‘V’
ppi_enrichment: no visible global function definition for ‘ecount’
ppi_enrichment: no visible global function definition for
  ‘induced.subgraph’
ppi_enrichment: no visible global function definition for ‘degree’
ppi_enrichment_full: no visible global function definition for ‘V’
ppi_enrichment_full: no visible global function definition for ‘ecount’
ppi_enrichment_full: no visible global function definition for
  ‘induced.subgraph’
ppi_enrichment_full: no visible global function definition for ‘degree’
ppie.getNumEdgesBetween: no visible global function definition for
  ‘neighborhood’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* 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 data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘STRINGdb-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: STRINGdb-package
> ### Title: STRINGdb (an R interface to http://string-db.org)
> ### Aliases: \S4method{STRINGdb-package}{STRINGdb}
> ### Keywords: package
> 
> ### ** Examples
> 
> 
> library(STRINGdb)
> data(diff_exp_example1)
> 
> # create a new STRING_db object
> string_db <- STRINGdb$new()
WARNING: You didn't specify a species. Hence we will set 9606 (Homo Sapiens) as your species.
WARNING: You didn't specify a version of the STRING database to use. Hence we will use STRING 9_1.
> 
> # map to STRING
> example1_mapped = string_db$map( diff_exp_example1, "gene", removeUnmappedRows = TRUE )
trying URL 'http://string.uzh.ch/permanent/string/9_1/protein_aliases/9606__protein_aliases_tf.tsv.gz'
Content type 'application/x-gzip' length 12814734 bytes (12.2 MB)
opened URL
==================================================
downloaded 12.2 MB

trying URL 'http://string.uzh.ch/permanent/string/9_1/proteins/9606__proteins.tsv.gz'
Content type 'application/x-gzip' length 1826579 bytes (1.7 MB)
opened URL
==================================================
downloaded 1.7 MB

Warning:  we couldn't map to STRING 17% of your identifiers> 
> # get the best 200 hits
> hits = example1_mapped$STRING_id[1:200]  
> 
> # plot the STRING network png 
> string_db$plot_network( hits )
trying URL 'http://string.uzh.ch/permanent/string/9_1/protein_links/9606__protein_links.tsv.gz'
Content type 'application/x-gzip' length 18915936 bytes (18.0 MB)
opened URL
==================================================
downloaded 18.0 MB

> 
> # plot a protein-protein enrichment graph of the best 1000 hits in order to see how the ppi signal is distributed along the sorted list
> string_db$plot_ppi_enrichment( example1_mapped$STRING_id[1:1000] )

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=                                                                     |   2%
  |                                                                            
  |===                                                                   |   4%
  |                                                                            
  |====                                                                  |   6%
  |                                                                            
  |======                                                                |   8%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |========                                                              |  12%
  |                                                                            
  |==========                                                            |  14%
  |                                                                            
  |===========                                                           |  16%
  |                                                                            
  |=============                                                         |  18%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |===============                                                       |  22%
  |                                                                            
  |=================                                                     |  24%
  |                                                                            
  |==================                                                    |  26%
  |                                                                            
  |====================                                                  |  28%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |======================                                                |  32%
  |                                                                            
  |========================                                              |  34%
  |                                                                            
  |=========================                                             |  36%
  |                                                                            
  |===========================                                           |  38%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |=============================                                         |  42%
  |                                                                            
  |===============================                                       |  44%
  |                                                                            
  |================================                                      |  46%
  |                                                                            
  |==================================                                    |  48%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |====================================                                  |  52%
  |                                                                            
  |======================================                                |  54%
  |                                                                            
  |=======================================                               |  56%
  |                                                                            
  |=========================================                             |  58%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |===========================================                           |  62%
  |                                                                            
  |=============================================                         |  64%
  |                                                                            
  |==============================================                        |  66%
  |                                                                            
  |================================================                      |  68%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |==================================================                    |  72%
  |                                                                            
  |====================================================                  |  74%
  |                                                                            
  |=====================================================                 |  76%
  |                                                                            
  |=======================================================               |  78%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |=========================================================             |  82%
  |                                                                            
  |===========================================================           |  84%
  |                                                                            
  |============================================================          |  86%
  |                                                                            
  |==============================================================        |  88%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |================================================================      |  92%
  |                                                                            
  |==================================================================    |  94%
  |                                                                            
  |===================================================================   |  96%
  |                                                                            
  |===================================================================== |  98%
  |                                                                            
  |======================================================================| 100%
> 
> 
> ######## use the "halo" mechanism in STRING to distinguish between down and up-regulated genes  ########
> 
> # filter by p-value and add a color column (i.e. green down-regulated gened and red for up-regulated genes)
> example1_mapped_pval05 = string_db$add_diff_exp_color( subset(example1_mapped, pvalue<0.05), logFcColStr="logFC" )    
> 
> # post payload information to the STRING server
> payload_id = string_db$post_payload( example1_mapped_pval05$STRING_id, colors=example1_mapped_pval05$color )
> 
> # display a STRING network png with the "halo"
> string_db$plot_network( hits, payload_id=payload_id )
> 
> 
> ######## compute enrichment in GO annotations  ########
> enrichmentGO = string_db$get_enrichment( hits, category = "Process", methodMT = "fdr", iea = TRUE )
trying URL 'http://string.uzh.ch/permanent/string/9_1/enrichment_annotations/annotations/annotations_9606.tsv.gz'
Content type 'application/x-gzip' length 21476039 bytes (20.5 MB)
opened URL
==================================================
downloaded 20.5 MB

Loading required package: tcltk
trying URL 'http://string.uzh.ch/permanent/string/9_1/enrichment_annotations/annotations_description/annotations_description.tsv.gz'
Content type 'application/x-gzip' length 24278820 bytes (23.2 MB)
opened URL
==================================================
downloaded 23.2 MB

> enrichmentKEGG = string_db$get_enrichment( hits, category = "KEGG", methodMT = "fdr", iea = TRUE )
> head(enrichmentGO, n=7)
     term_id proteins hits       pvalue  pvalue_fdr
1 GO:0006952     1181   25 8.429187e-07 0.001672707
2 GO:0052547      301   12 1.616923e-06 0.001672707
3 GO:0043207      576   16 3.407698e-06 0.001762632
4 GO:0051707      576   16 3.407698e-06 0.001762632
5 GO:0010466      180    9 5.536201e-06 0.001977537
6 GO:0009607      605   16 6.338179e-06 0.001977537
7 GO:0052548      288   11 6.690556e-06 0.001977537
                           term_description
1                          defense response
2          regulation of peptidase activity
3      response to external biotic stimulus
4                response to other organism
5 negative regulation of peptidase activity
6               response to biotic stimulus
7      regulation of endopeptidase activity
> head(enrichmentKEGG, n=7)
   term_id proteins hits       pvalue   pvalue_fdr
1 hsa00512      218   10 6.603565e-10 7.792207e-08
2 hsa04115       72    7 1.519531e-09 8.965232e-08
3 hsa04512      450   12 5.404541e-09 2.125786e-07
4 hsa00500       61    5 8.987697e-07 2.651371e-05
5 hsa00140      286    8 1.652849e-06 3.280367e-05
6 hsa04610       69    5 1.667983e-06 3.280367e-05
7 hsa04145      227    7 4.080518e-06 6.878588e-05
                      term_description
1     Mucin type O-Glycan biosynthesis
2                p53 signaling pathway
3             ECM-receptor interaction
4        Starch and sucrose metabolism
5         Steroid hormone biosynthesis
6  Complement and coagulation cascades
7                            Phagosome
> 
> 
> 
> ########  Use STRING in order to get homologous proteins in other species ########
> 
> # get the reciprocal best hits of the following protein in all the STRING species
> string_db$get_homologs_besthits(c("9606.ENSP00000365757"), symbets = TRUE)
              STRING_id species_id       best_hit_STRING_id best_hit_bitscore
1  9606.ENSP00000365757       6085        6085.XP_002161268             480.5
2  9606.ENSP00000365757       6238            6238.CBG15109             455.7
3  9606.ENSP00000365757       6239            6239.Y48G9A.8             476.6
4  9606.ENSP00000365757       6945       6945.ISCW009432-PA             467.2
5  9606.ENSP00000365757       7070           7070.XP_971403             572.6
6  9606.ENSP00000365757       7719  7719.ENSCINP00000013390             546.4
7  9606.ENSP00000365757       7955  7955.ENSDARP00000003352             816.7
8  9606.ENSP00000365757       8090  8090.ENSORLP00000009006             808.3
9  9606.ENSP00000365757       9031  9031.ENSGALP00000012779             791.9
10 9606.ENSP00000365757       9258  9258.ENSOANP00000009063             835.9
11 9606.ENSP00000365757       9361  9361.ENSDNOP00000012412             716.1
12 9606.ENSP00000365757       9544  9544.ENSMMUP00000019705             836.9
13 9606.ENSP00000365757       9598  9598.ENSPTRP00000003988             836.9
14 9606.ENSP00000365757       9600  9600.ENSPPYP00000002495             849.1
15 9606.ENSP00000365757       9606     9606.ENSP00000365757             944.1
16 9606.ENSP00000365757       9615  9615.ENSCAFP00000006237             836.9
17 9606.ENSP00000365757       9685  9685.ENSFCAP00000005093             750.0
18 9606.ENSP00000365757       9796  9796.ENSECAP00000006272             830.6
19 9606.ENSP00000365757       9823  9823.ENSSSCP00000011817             940.6
20 9606.ENSP00000365757       9913  9913.ENSBTAP00000024007             828.5
21 9606.ENSP00000365757       9986  9986.ENSOCUP00000014710             943.8
22 9606.ENSP00000365757      10090 10090.ENSMUSP00000006912             934.0
23 9606.ENSP00000365757      10141 10141.ENSCPOP00000006815             925.6
24 9606.ENSP00000365757      10228           10228.JGI22804             468.9
25 9606.ENSP00000365757      13616 13616.ENSMODP00000011260             931.2
26 9606.ENSP00000365757      28377 28377.ENSACAP00000008733             780.0
27 9606.ENSP00000365757      31033 31033.ENSTRUP00000005623             811.8
28 9606.ENSP00000365757      31234           31234.CRE02385             477.3
29 9606.ENSP00000365757      35128          35128.JGI264335             189.3
30 9606.ENSP00000365757      59729 59729.ENSTGUP00000001234             795.4
31 9606.ENSP00000365757      67593          67593.JGI138693             190.7
32 9606.ENSP00000365757      69293 69293.ENSGACP00000003246             794.3
33 9606.ENSP00000365757     135651          135651.CBN14981             476.3
34 9606.ENSP00000365757     281687          281687.CJA09616             425.6
35 9606.ENSP00000365757     317025          317025.Tcr_0057              53.8
   best_hit_normscore best_hit_alignment_length nr_high_scoring_hits
1           0.5089500                       396                    2
2           0.4826820                       391                    3
3           0.5048190                       392                    3
4           0.4948630                       359                    4
5           0.6065040                       409                    3
6           0.5787520                       391                    4
7           0.8650570                       403                   11
8           0.8561590                       404                   10
9           0.8387880                       357                    6
10          0.8853940                       382                    6
11          0.7585000                       357                    5
12          0.8864530                       357                    6
13          0.8864530                       357                    8
14          0.8993750                       362                    9
15          1.0000000                       405                    9
16          0.8864530                       357                    9
17          0.7944070                       404                    6
18          0.8797800                       357                    7
19          0.9962930                       405                    5
20          0.8775550                       356                    8
21          0.9996820                       405                    7
22          0.9893020                       404                    8
23          0.9804050                       402                    8
24          0.4966630                       386                    2
25          0.9863360                       405                    7
26          0.8261840                       356                    7
27          0.8598670                       404                   13
28          0.5055610                       385                    4
29          0.2005080                       323                    4
30          0.8424960                       357                    6
31          0.2019910                       294                   15
32          0.8413300                       403                   13
33          0.5045020                       392                    5
34          0.4508000                       406                    3
35          0.0569855                       205                    0
> 
> # get the homologs of the following two proteins in the mouse (i.e. species_id=10090)
> string_db$get_homologs(c("9606.ENSP00000365757", "9606.ENSP00000352336"), target_species_id=10090, bitscore_threshold=60)
            STRING_id_a              STRING_id_b bitscore start_a end_a start_b
1  9606.ENSP00000352336 10090.ENSMUSP00000003370     73.0     530   695     140
2  9606.ENSP00000352336 10090.ENSMUSP00000004377     76.2     531   722       4
3  9606.ENSP00000352336 10090.ENSMUSP00000004959     85.6     640   827      57
4  9606.ENSP00000352336 10090.ENSMUSP00000005889     85.9     646   826     671
5  9606.ENSP00000352336 10090.ENSMUSP00000006293     61.2     532   825      14
6  9606.ENSP00000352336 10090.ENSMUSP00000010804    303.8      30   478      28
7  9606.ENSP00000352336 10090.ENSMUSP00000014597     75.5     514   680      99
8  9606.ENSP00000352336 10090.ENSMUSP00000016498     66.7     638   739     127
9  9606.ENSP00000352336 10090.ENSMUSP00000016511     65.3     642   734      74
10 9606.ENSP00000352336 10090.ENSMUSP00000017920     66.4     637   830       4
11 9606.ENSP00000352336 10090.ENSMUSP00000019913     70.6     511   649     101
12 9606.ENSP00000352336 10090.ENSMUSP00000020564     61.2     454   631     367
13 9606.ENSP00000352336 10090.ENSMUSP00000021090     96.8     640   828      57
14 9606.ENSP00000352336 10090.ENSMUSP00000025912    192.1     810  1198     479
15 9606.ENSP00000352336 10090.ENSMUSP00000025962    223.8     207  1182    1269
16 9606.ENSP00000352336 10090.ENSMUSP00000027888     67.8     517   648     157
17 9606.ENSP00000352336 10090.ENSMUSP00000028252     61.9     526   618     431
18 9606.ENSP00000352336 10090.ENSMUSP00000029806     64.6     646   769      35
19 9606.ENSP00000352336 10090.ENSMUSP00000030464     75.5     370   640     198
20 9606.ENSP00000352336 10090.ENSMUSP00000030693     71.3     517   621     116
21 9606.ENSP00000352336 10090.ENSMUSP00000032356    219.0     145   487      13
22 9606.ENSP00000352336 10090.ENSMUSP00000032931     61.5     731   831     549
23 9606.ENSP00000352336 10090.ENSMUSP00000033468     71.3     771   888     185
24 9606.ENSP00000352336 10090.ENSMUSP00000034296     67.8     637   795     315
25 9606.ENSP00000352336 10090.ENSMUSP00000034745     62.2     767   827    1050
26 9606.ENSP00000352336 10090.ENSMUSP00000034863     65.3     532   806      82
27 9606.ENSP00000352336 10090.ENSMUSP00000036270    107.6     635   826     661
28 9606.ENSP00000352336 10090.ENSMUSP00000037854    245.8       4   478      13
29 9606.ENSP00000352336 10090.ENSMUSP00000038838     74.4     530   673     127
30 9606.ENSP00000352336 10090.ENSMUSP00000046532     80.7     512   824      41
31 9606.ENSP00000352336 10090.ENSMUSP00000046584    262.3      48   478     169
32 9606.ENSP00000352336 10090.ENSMUSP00000048057     60.5     636   754       8
33 9606.ENSP00000352336 10090.ENSMUSP00000056774     67.4     641   735     619
34 9606.ENSP00000352336 10090.ENSMUSP00000058757    107.9     531   787       5
35 9606.ENSP00000352336 10090.ENSMUSP00000059658     63.6     642   735     389
36 9606.ENSP00000352336 10090.ENSMUSP00000060433     61.9     626   740     384
37 9606.ENSP00000352336 10090.ENSMUSP00000060828     74.4     641   862     162
38 9606.ENSP00000352336 10090.ENSMUSP00000062782     94.0     634   826     647
39 9606.ENSP00000352336 10090.ENSMUSP00000066209     69.5     433   790      47
40 9606.ENSP00000352336 10090.ENSMUSP00000066361     63.2     763   831    1149
41 9606.ENSP00000352336 10090.ENSMUSP00000072154     69.9     517   638     140
42 9606.ENSP00000352336 10090.ENSMUSP00000072840     69.5     778   909       8
43 9606.ENSP00000352336 10090.ENSMUSP00000075167     70.6     517   648     130
44 9606.ENSP00000352336 10090.ENSMUSP00000079991   2832.2       1  1265       1
45 9606.ENSP00000352336 10090.ENSMUSP00000081122    313.9      54  1243      53
46 9606.ENSP00000352336 10090.ENSMUSP00000084679     60.8     759   827     436
47 9606.ENSP00000352336 10090.ENSMUSP00000091940     62.6     518   635     470
48 9606.ENSP00000352336 10090.ENSMUSP00000092252     62.6    1027  1161       1
49 9606.ENSP00000352336 10090.ENSMUSP00000097547     76.9     517   680     133
50 9606.ENSP00000352336 10090.ENSMUSP00000099366    280.8      67   480     107
51 9606.ENSP00000352336 10090.ENSMUSP00000099404   1468.2      11  1242      18
52 9606.ENSP00000352336 10090.ENSMUSP00000099583    185.8      54   457      49
53 9606.ENSP00000352336 10090.ENSMUSP00000101256    329.6      21  1182     122
54 9606.ENSP00000352336 10090.ENSMUSP00000104860     62.6     637   765     236
55 9606.ENSP00000352336 10090.ENSMUSP00000105155     62.2     517   666     140
56 9606.ENSP00000352336 10090.ENSMUSP00000105179     85.6     506   883     149
57 9606.ENSP00000352336 10090.ENSMUSP00000105189     60.1     532   680      93
58 9606.ENSP00000352336 10090.ENSMUSP00000105736    216.2      52   460      48
59 9606.ENSP00000352336 10090.ENSMUSP00000105743    193.8      54   457      54
60 9606.ENSP00000352336 10090.ENSMUSP00000106539     70.2     771   965     165
61 9606.ENSP00000352336 10090.ENSMUSP00000109234     65.3     646   858     150
62 9606.ENSP00000352336 10090.ENSMUSP00000109377    272.0      65   480      61
63 9606.ENSP00000352336 10090.ENSMUSP00000112221     61.9     645   726     281
64 9606.ENSP00000352336 10090.ENSMUSP00000117099     64.3     632   740     335
65 9606.ENSP00000352336 10090.ENSMUSP00000118491     62.2     759   827     404
66 9606.ENSP00000365757 10090.ENSMUSP00000006912    934.0       1   405       1
67 9606.ENSP00000365757 10090.ENSMUSP00000013970    600.2      16   405      26
68 9606.ENSP00000365757 10090.ENSMUSP00000018691    743.4      13   406      18
69 9606.ENSP00000365757 10090.ENSMUSP00000025800    199.4      33   401      25
70 9606.ENSP00000365757 10090.ENSMUSP00000038225    195.2      34   401      76
71 9606.ENSP00000365757 10090.ENSMUSP00000051282    119.8      98   397     107
72 9606.ENSP00000365757 10090.ENSMUSP00000102852    199.4      34   401      68
73 9606.ENSP00000365757 10090.ENSMUSP00000109676     88.0      91   282    1773
   end_b size_b
1    285    524
2    197    596
3    215    217
4    839    845
5    292    303
6    471    756
7    246    499
8    231    507
9    169    451
10   193    304
11   237    512
12   540    548
13   214    217
14   857   1234
15  1963   2282
16   272   1182
17   519    538
18   164    280
19   457    461
20   218    517
21   333    647
22   655    764
23   305    788
24   475    722
25  1107   1107
26   352    450
27   845    847
28   487   1015
29   252    512
30   317    322
31   596   1128
32   136   1257
33   718    724
34   272    597
35   488    492
36   503    503
37   388    629
38   864    868
39   354    509
40  1214   1719
41   258    541
42   137    709
43   245   1142
44  1265   1265
45   920   1682
46   508    513
47   575    579
48   126    825
49   282    537
50   503    785
51  1267   1302
52   464   1181
53   958   1501
54   368    625
55   273    541
56   558   1038
57   248    259
58   467   1175
59   468   1216
60   371    862
61   380    527
62   456    807
63   362    377
64   446    446
65   476    481
66   405    405
67   420    421
68   416    416
69   391    539
70   439    661
71   386    395
72   431    547
73  1979   2052
> 
> 
> 
> ########  Retrieve protein-protein interactions ########
> 
> # get the neighbors (in the ppi graph) of a given protein(s)
> string_db$get_neighbors(c("9606.ENSP00000365757", "9606.ENSP00000352336"))
  [1] "9606.ENSP00000007390" "9606.ENSP00000162749" "9606.ENSP00000171887"
  [4] "9606.ENSP00000195649" "9606.ENSP00000201586" "9606.ENSP00000211998"
  [7] "9606.ENSP00000216117" "9606.ENSP00000216277" "9606.ENSP00000219789"
 [10] "9606.ENSP00000221283" "9606.ENSP00000222124" "9606.ENSP00000222254"
 [13] "9606.ENSP00000223023" "9606.ENSP00000225504" "9606.ENSP00000225655"
 [16] "9606.ENSP00000230124" "9606.ENSP00000230449" "9606.ENSP00000230859"
 [19] "9606.ENSP00000234313" "9606.ENSP00000239940" "9606.ENSP00000240132"
 [22] "9606.ENSP00000240139" "9606.ENSP00000240327" "9606.ENSP00000243924"
 [25] "9606.ENSP00000244007" "9606.ENSP00000246062" "9606.ENSP00000249071"
 [28] "9606.ENSP00000249647" "9606.ENSP00000249700" "9606.ENSP00000249861"
 [31] "9606.ENSP00000250699" "9606.ENSP00000252699" "9606.ENSP00000253083"
 [34] "9606.ENSP00000253861" "9606.ENSP00000254806" "9606.ENSP00000255039"
 [37] "9606.ENSP00000255882" "9606.ENSP00000256190" "9606.ENSP00000259271"
 [40] "9606.ENSP00000260257" "9606.ENSP00000260386" "9606.ENSP00000260402"
 [43] "9606.ENSP00000260762" "9606.ENSP00000260766" "9606.ENSP00000261349"
 [46] "9606.ENSP00000261776" "9606.ENSP00000262033" "9606.ENSP00000262039"
 [49] "9606.ENSP00000262139" "9606.ENSP00000262445" "9606.ENSP00000262713"
 [52] "9606.ENSP00000262717" "9606.ENSP00000262741" "9606.ENSP00000263125"
 [55] "9606.ENSP00000263168" "9606.ENSP00000263967" "9606.ENSP00000264380"
 [58] "9606.ENSP00000264414" "9606.ENSP00000264710" "9606.ENSP00000265382"
 [61] "9606.ENSP00000265741" "9606.ENSP00000265960" "9606.ENSP00000266087"
 [64] "9606.ENSP00000266505" "9606.ENSP00000267101" "9606.ENSP00000267615"
 [67] "9606.ENSP00000269025" "9606.ENSP00000269159" "9606.ENSP00000269300"
 [70] "9606.ENSP00000269321" "9606.ENSP00000270202" "9606.ENSP00000271657"
 [73] "9606.ENSP00000272102" "9606.ENSP00000272298" "9606.ENSP00000272427"
 [76] "9606.ENSP00000274335" "9606.ENSP00000275198" "9606.ENSP00000276410"
 [79] "9606.ENSP00000278279" "9606.ENSP00000279230" "9606.ENSP00000281038"
 [82] "9606.ENSP00000282074" "9606.ENSP00000284384" "9606.ENSP00000284523"
 [85] "9606.ENSP00000285419" "9606.ENSP00000285600" "9606.ENSP00000286317"
 [88] "9606.ENSP00000286428" "9606.ENSP00000289153" "9606.ENSP00000290846"
 [91] "9606.ENSP00000291295" "9606.ENSP00000292807" "9606.ENSP00000295024"
 [94] "9606.ENSP00000295057" "9606.ENSP00000296003" "9606.ENSP00000296794"
 [97] "9606.ENSP00000297029" "9606.ENSP00000298229" "9606.ENSP00000298316"
[100] "9606.ENSP00000298642" "9606.ENSP00000298841" "9606.ENSP00000300935"
[103] "9606.ENSP00000302005" "9606.ENSP00000302276" "9606.ENSP00000303476"
[106] "9606.ENSP00000304283" "9606.ENSP00000305011" "9606.ENSP00000305958"
[109] "9606.ENSP00000306124" "9606.ENSP00000306382" "9606.ENSP00000307183"
[112] "9606.ENSP00000307356" "9606.ENSP00000307684" "9606.ENSP00000308176"
[115] "9606.ENSP00000308622" "9606.ENSP00000310969" "9606.ENSP00000312734"
[118] "9606.ENSP00000313121" "9606.ENSP00000313731" "9606.ENSP00000314311"
[121] "9606.ENSP00000314458" "9606.ENSP00000316029" "9606.ENSP00000317334"
[124] "9606.ENSP00000317985" "9606.ENSP00000319322" "9606.ENSP00000319511"
[127] "9606.ENSP00000319601" "9606.ENSP00000319654" "9606.ENSP00000320025"
[130] "9606.ENSP00000322170" "9606.ENSP00000322234" "9606.ENSP00000323377"
[133] "9606.ENSP00000323927" "9606.ENSP00000324806" "9606.ENSP00000325423"
[136] "9606.ENSP00000326514" "9606.ENSP00000328773" "9606.ENSP00000329127"
[139] "9606.ENSP00000331313" "9606.ENSP00000331602" "9606.ENSP00000334105"
[142] "9606.ENSP00000334416" "9606.ENSP00000334490" "9606.ENSP00000335333"
[145] "9606.ENSP00000338185" "9606.ENSP00000339826" "9606.ENSP00000340017"
[148] "9606.ENSP00000340093" "9606.ENSP00000340896" "9606.ENSP00000341243"
[151] "9606.ENSP00000341680" "9606.ENSP00000342510" "9606.ENSP00000342935"
[154] "9606.ENSP00000344488" "9606.ENSP00000344818" "9606.ENSP00000345083"
[157] "9606.ENSP00000345206" "9606.ENSP00000345988" "9606.ENSP00000346453"
[160] "9606.ENSP00000347198" "9606.ENSP00000347244" "9606.ENSP00000347792"
[163] "9606.ENSP00000347931" "9606.ENSP00000348010" "9606.ENSP00000348461"
[166] "9606.ENSP00000348602" "9606.ENSP00000348984" "9606.ENSP00000348986"
[169] "9606.ENSP00000349205" "9606.ENSP00000349275" "9606.ENSP00000349467"
[172] "9606.ENSP00000350649" "9606.ENSP00000350698" "9606.ENSP00000350928"
[175] "9606.ENSP00000350941" "9606.ENSP00000351190" "9606.ENSP00000351997"
[178] "9606.ENSP00000352035" "9606.ENSP00000352121" "9606.ENSP00000352312"
[181] "9606.ENSP00000352336" "9606.ENSP00000352834" "9606.ENSP00000353154"
[184] "9606.ENSP00000353275" "9606.ENSP00000353422" "9606.ENSP00000354519"
[187] "9606.ENSP00000354558" "9606.ENSP00000354947" "9606.ENSP00000354977"
[190] "9606.ENSP00000355537" "9606.ENSP00000355596" "9606.ENSP00000356989"
[193] "9606.ENSP00000357583" "9606.ENSP00000357674" "9606.ENSP00000357748"
[196] "9606.ENSP00000357883" "9606.ENSP00000359025" "9606.ENSP00000359417"
[199] "9606.ENSP00000359423" "9606.ENSP00000359425" "9606.ENSP00000359665"
[202] "9606.ENSP00000360076" "9606.ENSP00000360154" "9606.ENSP00000360473"
[205] "9606.ENSP00000360777" "9606.ENSP00000361021" "9606.ENSP00000362115"
[208] "9606.ENSP00000362399" "9606.ENSP00000362924" "9606.ENSP00000364287"
[211] "9606.ENSP00000365103" "9606.ENSP00000365637" "9606.ENSP00000365687"
[214] "9606.ENSP00000366272" "9606.ENSP00000366460" "9606.ENSP00000366563"
[217] "9606.ENSP00000367075" "9606.ENSP00000367276" "9606.ENSP00000367415"
[220] "9606.ENSP00000367747" "9606.ENSP00000367792" "9606.ENSP00000368086"
[223] "9606.ENSP00000370912" "9606.ENSP00000371221" "9606.ENSP00000371577"
[226] "9606.ENSP00000373347" "9606.ENSP00000373399" "9606.ENSP00000373648"
[229] "9606.ENSP00000373713" "9606.ENSP00000375928" "9606.ENSP00000376440"
[232] "9606.ENSP00000376946" "9606.ENSP00000376966" "9606.ENSP00000377148"
[235] "9606.ENSP00000377941" "9606.ENSP00000378306" "9606.ENSP00000378323"
[238] "9606.ENSP00000379372" "9606.ENSP00000379709" "9606.ENSP00000381102"
[241] "9606.ENSP00000381293" "9606.ENSP00000383457" "9606.ENSP00000384651"
[244] "9606.ENSP00000388631" "9606.ENSP00000389934" "9606.ENSP00000392147"
[247] "9606.ENSP00000393835" "9606.ENSP00000397181" "9606.ENSP00000398036"
[250] "9606.ENSP00000407333" "9606.ENSP00000408089" "9606.ENSP00000409572"
[253] "9606.ENSP00000409637" "9606.ENSP00000413780" "9606.ENSP00000414138"
[256] "9606.ENSP00000416320" "9606.ENSP00000418111"
> 
> # get the interactions in between the input proteins
> string_db$get_interactions(c("9606.ENSP00000365757", "9606.ENSP00000352336"))
                  from                   to neighborhood fusion cooccurence
1 9606.ENSP00000352336 9606.ENSP00000365757            0      0           0
  coexpression experimental database textmining combined_score
1            0            0      900         76            901
> 
> 
> 
> ######## Find clusters of interactions ########
> 
> # get clusters
> clustersList = string_db$get_clusters(example1_mapped$STRING_id[1:600])
> 
> # plot first 4 clusters
> par(mfrow=c(2,2))
> for(i in seq(1:4)){
+   string_db$plot_network(clustersList[[i]])
+ }
Error: Proxy Error
Execution halted

STRINGdb.Rcheck/00install.out:

* installing *source* package ‘STRINGdb’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (STRINGdb)

STRINGdb.Rcheck/STRINGdb-Ex.timings:

nameusersystemelapsed
STRINGdb-class0.0050.0000.006